complete course in astrobiology (physics textbook)

Complete Course in Astrobiology

Edited by

Gerda Horneck and Petra Rettberg

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Complete Course in Astrobiology

Edited byGerda Horneck and Petra Rettberg

The Editors

Dr. Gerda HorneckDLRInst. of Aerospace Medicine51170 Kçln

Dr. Petra RettbergDLRInst. of Aerospace Medicine51147 Kçln

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Table of Contents

1 Astrobiology: From the Origin of Life on Earth to Life in the UniverseAndr� Brack

1.1 General Aspects of Astrobiology 11.1.1 Historical Milestones 11.1.2 Searching for Emerging Life 31.1.3 The Role of Water 41.1.4 The Physicochemical Features of Carbon-based Life 41.1.5 Clays as Possible Primitive Robots 61.2 Reconstructing Life in a Test Tube 71.2.1 The Quest for Organic Molecules 71.2.1.1 Terrestrial Production 71.2.1.2 Delivery of Extraterrestrial Organic Molecules 81.2.2 Space Experiments 101.2.3 Attempts to Recreate Life in a Test Tube 111.2.4 A Primitive Life Simpler than a Cell? 131.3 The Search for Traces of Primitive Life 141.3.1 Microfossils 141.3.2 Oldest Sedimentary Rocks 151.4 The Search for Life in the Solar System 151.4.1 Planet Mars and the SNC Meteorites 151.4.2 Jupiter’s Moon Europa 171.4.3 Saturn’s Moon Titan 181.5 The Search for Life Beyond the Solar System 191.5.1 The Search for Rocky Earthlike Exoplanets 191.5.2 Detecting Extrasolar Life 201.6 Conclusions 201.7 Further Reading 211.7.1 Books and Articles in Books 211.7.2 Articles in Journals 211.7.3 Web Sites 22

V

Complete Course in Astrobiology. Edited by Gerda Horneck and Petra RettbergCopyright � 2007 WILEY-VCH Verlag GmbH & Co. KGaA, WeinheimISBN: 978-3-527-40660-9

2 From the Big Bang to the Molecules of LifeHarry J. Lehto

2.1 Building Blocks of Life 232.2 Big Bang: Formation of H and He 252.3 First Stars: Formation of Small Amounts of C, O, N, S and P and

Other Heavy Elements 282.4 Normal Modern Stars, Bulk Formation of C, O, N, S, P and Other

Heavy Elements 292.5 The First Molecules (CO and H2O) 352.6 Interstellar Matter 352.6.1 Interstellar Clouds 372.6.2 Interstellar Grains 392.6.2.1 Formation 392.6.2.2 Observed Properties 402.6.3 Ices 412.6.4 Molecules in the Gas Phase 422.6.4.1 Observed Properties 422.6.4.2 Formation of H2 432.6.4.3 Formation of CO and H2O 442.7 Generation of Stars: Formation of the Sun and Planets 442.7.1 Accretion Disk of the Sun 442.7.2 Formation of the Earth 462.7.3 Early Rain ofMeteorites, Comets, Asteroids, and PrebioticMolecules 472.7.4 D/H Ratio and Oceans 492.8 Further Reading 512.8.1 Books or Articles in Books 512.8.2 Articles in Journals 512.8.3 Web Sites 532.9 Questions for Students 53

3 Basic Prebiotic ChemistryHerv� Cottin

3.1 Key Molecules of Life 553.1.1 Dismantling the Robots 563.1.2 Proteins and Amino Acids 583.1.3 DNA, RNA, and Their Building Blocks 603.1.4 First “Prebiotic Robot” 633.2 Historical Milestones 633.3 Sources of Prebiotic Organic Molecules 693.3.1 Endogenous Sources of Organic Molecules 693.3.1.1 Atmospheric Syntheses 693.3.1.2 Hydrothermal Vents 703.3.2 Exogenous Delivery of Organic Molecules 713.3.2.1 Comets 713.3.2.2 Meteorites 73

Table of ContentsVI

3.3.2.3 Micrometeorites 743.3.3 Relative Contribution of the Different Sources 743.4 From Simple to Slightly More Complex Compounds 753.4.1 Synthesis of Amino Acids 753.4.2 Synthesis of Purine and Pyrimidine Bases 763.4.3 Synthesis of Sugars 783.4.4 Synthesis of Polymers 803.5 Conclusions 813.6 Further Reading 823.6.1 Books or Articles in Books 823.6.2 Articles in Journals 823.7 Questions for Students 833.7.1 Basic-level Questions 833.7.2 Advanced-level Questions 83

4 From Molecular Evolution to Cellular LifeKirsi Lehto

4.1 History of Life at Its Beginnings 854.2 Life as It Is Known 884.2.1 The Phylogenetic Tree of Life 884.2.2 Life is Cellular, Happens in Liquid Water, and Is Based on

Genetic Information 884.2.2.1 Genetic Information 924.2.2.2 The Genetic Code and Its Expression 944.3 Last Universal Common Ancestor (LUCA) 964.3.1 Containment in a Cell Membrane 974.3.2 Genes and Their Expression 994.3.3 Hypothetical Structure of the LUCA Genome 1034.4 “Life” in the RNA–Protein World: Issues and Possible Solutions 1054.4.1 Evolutionary Solutions 1064.4.2 Solutions Found in the Viral World 1074.5 “Life” Before the Appearance of the Progenote 1084.5.1 The Breakthrough Organism and the RNA–Protein World 1084.5.2 Primitive Translation Machinery 1084.5.3 Origin of Ribosomes 1094.6 The RNA World 1114.6.1 Origin of the RNA World 1134.6.1.1 Prebiotic Assembly of Polymers 1134.6.1.2 The Building Blocks of the RNA World 1144.6.1.3 Where Could the RNA World Exist and Function? 1154.7 Beginning of Life 1174.8 Further Reading 1184.8.1 Books 1184.8.2 Articles in Journals 1184.9 Questions for Students 120

Table of Contents VII

5 Extremophiles, the Physicochemical Limits of Life (Growth and Survival)Helga Stan-Lotter

5.1 A Brief History of Life on Earth 1215.1.1 Early Earth and Microfossils 1215.1.2 Prokaryotes, Eukaryotes, and the Tree of Life 1235.1.3 Some Characteristics of Bacteria and Archaea 1265.1.3.1 Cell Walls, Envelopes, and Shape 1265.1.3.2 Lipids and Membranes 1275.2 Extremophiles and Extreme Environments 1275.2.1 Growth versus Survival 1295.2.2 The Search for Life on Mars: The Viking Mission 1305.2.3 Temperature Ranges for Microorganisms 1325.2.4 High-temperature Environments 1335.2.4.1 Geography and Isolates 1335.2.4.2 Molecular Properties of Hyperthermophiles 1365.2.4.3 Early Evolution and Hyperthermophiles 1375.2.4.4 Applications 1385.2.5 Low-temperature Environments 1385.2.5.1 Geography and Isolates 1385.2.5.2 Molecular Adaptations 1395.2.6 Barophiles or Piezophiles 1405.2.7 High-salt Environments 1405.2.7.1 Hypersaline Environments and Isolates 1405.2.7.2 Viable Haloarchaea from Rock Salt 1415.2.7.3 Molecular Mechanisms 1425.2.7.4 Extraterrestrial Halite 1435.2.8 Subterranean Environments 1445.2.9 Radiation 1455.3 Microbial Survival of Extreme Conditions 1465.4 Conclusions 1485.5 Further Reading 1495.5.1 Books or Articles in Books 1495.5.2 Articles in Journals 1495.5.3 Web Sites 1505.6 Questions for Students 150

6 HabitabilityCharles S. Cockell

6.1 A Brief History of the Assessment of Habitability 1516.2 What Determines Habitability? 1546.3 Uninhabited Habitable Worlds 1566.4 Factors Determining Habitability 1566.4.1 Habitability and Temperature 1566.4.2 Habitability and Energy 1606.4.3 Other Factors that Determine Habitability 164

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6.5 A Postulate for Habitability 1656.5.1 Assumptions about the Habitat 1676.5.2 Assumptions on Life 1676.5.3 Attempt to Formulate a Habitability Postulate 1676.6 Some Test Cases for Habitability 1696.6.1 Test Case One: Life on Venus 1696.6.2 Test Case Two: Life on the Early Earth 1716.6.3 R�sum� of the Two Test Cases 1736.7 Conclusions 1736.8 Further Reading 1746.8.1 Books and Articles in Books 1746.8.2 Articles in Journals 1746.9 Questions for Students 176

7 Astrodynamics and Technological Aspects of Astrobiology Missionsin Our Solar SystemStefanos Fasoulas and Tino Schmiel

7.1 Introduction 1797.2 The Rocket Equation 1807.2.1 Single-staged Rockets 1807.2.2 Multiple-staged Rockets 1837.3 Orbital Mechanics and Astrodynamics 1847.3.1 Some Historical Notes 1847.3.2 The Energy Conservation Equation 1877.3.3 Some Typical Velocities 1887.4 Orbital Maneuvers 1907.4.1 High-thrust Maneuvers 1907.4.2 Low-thrust Maneuvers 1927.4.3 Gravity-assist Maneuvers 1937.5 Example: Missions to Mars 1957.6 Further Reading 2007.7 Questions for Students 200

8 Astrobiology of the Terrestrial Planets, with Emphasis on MarsMonica M. Grady

8.1 The Solar System 2038.2 Terrestrial Planets 2068.2.1 Mercury 2068.2.2 Venus 2078.2.3 Earth 2088.2.4 Mars 2088.2.4.1 Observing Mars 2088.2.4.2 Evidence for Water 2108.2.4.3 Evidence of Heat 2138.2.5 Meteorites from Mars 213

Table of Contents IX

8.2.5.1 Why from Mars? 2138.2.5.2 What can we Learn About Mars from Martian Meteorites? 2168.2.5.3 Microfossils in a Martian Meteorite? 2188.2.6 Can We Detect Signatures of Life on Mars? 2198.2.7 Conclusions: Life Beyond Earth? 2208.3 Further Reading 2208.3.1 Concerning Planetary Formation and Chronology 2208.3.2 Concerning Recent Results from Mars 2218.3.3 Concerning Terrestrial and Martian Microfossils 2218.3.4 Concerning Meteorites from Mars 2218.4 Questions for Students 222

9 Astrobiology of Saturn’s Moon TitanFranÅois Raulin

9.1 Extraterrestrial Bodies of Astrobiological Interest 2239.2 Some Historical Milestones in the Exploration of Titan 2259.3 General Properties, Formation and Internal Structure of Titan 2269.3.1 Main Properties 2269.3.2 Models of Formation and Internal Structure 2279.4 Atmosphere and Surface of Titan 2299.4.1 Theoretical Modeling of Titan’s Atmosphere 2299.4.2 Experimental Approach 2339.4.3 Observational Approach 2369.5 Astrobiological Aspects of Titan 2419.5.1 Analogies with Planet Earth 2419.5.2 Organic Chemistry 2429.5.3 Life on Titan? 2469.6 Outlook: Astrobiology and Future Exploration of Titan 2479.7 Further Reading 2499.7.1 Books and Articles in Books 2499.7.2 Articles in Journals 2509.7.3 Web Sites 2509.8 Questions for Students 251

10 Jupiter’s Moon Europa: Geology and HabitabilityChristophe Sotin and Daniel Prieur

10.1 A Short Survey of the Past Exploration of Europa 25310.2 Geology of the Moon Europa 25510.2.1 Surface Features 25510.2.2 Composition of the Surface 25710.3 Internal Structure of the Moon Europa 25810.4 Models of Evolution of the Moon Europa 26010.5 Astrobiological Considerations about Possibilities for Life

on the Moon Europa 26310.6 Summary and Conclusions 267

Table of ContentsX

10.7 Outlook and Plans for Future Missions 26810.8 Further Reading 26910.8.1 Books and Articles in Books 26910.8.2 Articles in Journals 27010.8.3 Web Sites 27110.9 Questions for Students 271

11 Astrobiology Experiments in Low Earth Orbit: Facilities,Instrumentation, and ResultsPietro Baglioni, Massimo Sabbatini, and Gerda Horneck

11.1 Low Earth Orbit Environment, a Test Bed for Astrobiology 27311.1.1 Cosmic Radiation Field in LEO 27511.1.1.1 Galactic Cosmic Radiation 27611.1.1.2 Solar Cosmic Radiation 27711.1.1.3 Radiation Belts 27811.1.2 Solar Extraterrestrial UV Radiation 27911.1.3 Space Vacuum 28011.1.4 Temperature Extremes 28011.1.5 Microgravity 28111.2 Astrobiology Questions Tackled by Experiments in Earth Orbit 28111.3 Exposure Facilities for Astrobiology Experiments 28211.3.1 BIOPAN 28311.3.1.1 Technical Characteristics of BIOPAN 28311.3.1.2 Experiment Hardware Accommodated within BIOPAN 28511.3.1.3 Operational Aspects of BIOPAN 28811.3.1.4 Orbital Characteristics of a BIOPAN Mission 29111.3.1.5 Environment of BIOPAN Experiments 29211.3.2 STONE 29311.3.3 EXPOSE 29511.3.3.1 EXPOSE Facility 29511.3.3.2 EXPOSE Experiments 29711.3.3.3 EXPOSE Experiment Hardware 29911.3.3.4 EXPOSE-R and EXPOSE-E 30111.3.3.5 Process of Experiment Proposal, Acceptance, Preparation,

and Validation 30211.4 Results from Astrobiology Experiments in Earth Orbit 30311.4.1 Relevance of Extraterrestrial Organic Molecules for the Emergence

of Life 30411.4.2 Role of Solar UV Radiation in Evolutionary Processes Related

to Life 30611.4.2.1 Efficiency of the Stratospheric Ozone Layer to Protect

Our Biosphere 30611.4.3 Chances and Limits of Life Being Transported from One Body of

Our Solar System to Another or Beyond 30711.4.3.1 Effects of Space Vacuum 309

Table of Contents XI

11.4.3.2 Effects of Extraterrestrial Solar UV Radiation 31011.4.3.3 Effects of Galactic Cosmic Radiation 31111.4.3.4 Combined Effects of All Parameters of Space 31311.4.3.5 Time Scales of Interplanetary Transport of Life 31311.4.4 Radiation Dosimetry in Space 31411.5 Future Development and Applications of Exposure Experiments 31611.6 Further Reading 31711.6.1 Books and Articles in Books 31711.6.2 Articles in Journals 31811.6.3 ESA Online Archives 31911.7 Questions for Students 319

12 Putting Together an Exobiology Mission: The ExoMars ExampleJorge L. Vago and Gerhard Kminek

12.1 Background of the ExoMars Mission 32112.1.1 Searching for Life on Mars 32112.1.2 Exobiology Research at ESA 32212.1.2.1 The ESA Exobiology Science Team Study 32412.1.2.2 The 1999 Exobiology Announcement of Opportunity 32512.1.3 The AURORA and the ELIPS Program of ESA 32612.1.3.1 The 2003 Pasteur Call for Ideas 32612.1.3.2 Approval of the ExoMars Mission 32812.2 ExoMars Science Objectives 32812.2.1 Searching for Signs of Life 32812.2.1.1 Extinct Life 32812.2.1.2 Extant Life 33212.2.1.3 Search for Life: Conclusions 33412.2.2 Hazards for Human Operations on Mars 33412.2.3 Geophysics Measurements 33512.3 ExoMars Science Strategy 33512.4 ExoMars Mission Description 33712.4.1 The ExoMars Rover 33912.5 Outlook and Conclusions 34512.6 Further Reading 34612.6.1 Books and Articles in Books 34612.6.2 Articles in Journals 34612.7 Questions for Students 351

13 Astrobiology Exploratory Missions and Planetary Protection RequirementsGerda Horneck, Andr� Debus, Peter Mani, and J. Andrew Spry

13.1 Rationale and History of Planetary Protection 35313.2 Current Planetary Protection Guidelines 35513.2.1 Category I Missions 35713.2.2 Category II Missions 35713.2.3 Category III Missions 359

Table of ContentsXII

13.2.4 Category IV Missions 35913.2.5 Category V Missions 36013.2.6 Future Development of Planetary Protection Guidelines 36113.3 Implementation of Planetary Protection Guidelines 36213.3.1 Bioload Measurements 36313.3.2 Bioburden Reduction 36713.3.2.1 Surface Wiping with Biocleaning Agents 37113.3.2.2 Gamma Radiation Sterilization 37113.3.2.3 Dry-heat Sterilization 37213.3.2.4 Hydrogen Peroxide Vapor/Gas Plasma Sterilization 37213.3.3 Prevention of Recontamination 37313.4 Astrobiology Exploratory Missions of Concern to Planetary

Protection 37413.4.1 Missions to the Moon 37413.4.2 Missions to Mars 37613.4.2.1 Orbiters or Flyby Missions to Mars 37613.4.2.2 Landers or Rovers with in Situ Measurements 37813.4.2.3 Landers or Rovers with Martian Samples Returned to the Earth 38313.4.2.4 Human Missions to Mars 38713.4.3 Missions to Venus 38813.4.4 Missions to the Moons of the Giant Planets 38913.4.5 Missions to Asteroids or Comets 39013.5 Outlook: Future Tasks of Planetary Protection 39213.6 Further Reading 39413.6.1 Concerning COSPAR Planetary Protection Guidelines 39513.6.2 Concerning Handbooks and Standards on Planetary Protection 39513.6.3 Concerning Bioload of Spacecraft 39513.6.4 Concerning Lunar Missions 39613.6.5 Concerning Missions to Terrestrial Planets 39613.6.6 Concerning Missions to Jupiter’s Moon Europa 39713.7 Questions for students 397

Index 399

Table of Contents XIII

Table of ContentsXIV

Preface

Astrobiology is a relatively new research area that addresses questions that haveintrigued humans for a long time: “How did life originate?” “Are we alone in theUniverse?” “What is the future of life on Earth and in the Universe?” Thesequestions are jointly tackled by scientists converging from widely different fields,reaching from astrophysics to molecular biology and from planetology to ecology,among others.Whereas classical biological research has concentrated on the only example of

“life” so far known – life on Earth – astrobiology extends the boundaries ofbiological investigations beyond the Earth to other planets, comets, meteorites,and space at large. Focal points are the different steps of the evolutionary pathwaysthrough cosmic history that may be related to the origin, evolution, and distribu-tion of life. In the interstellar medium, as well as in comets and meteorites,complex organics are detected in huge reservoirs that eventually may provide thechemical ingredients for life. More and more data on the existence of planetarysystems in our Galaxy are being acquired that support the assumption thathabitable zones are frequent and are not restricted to our own Solar System.From the extraordinary ability of life to adapt to environmental extremes, theboundary conditions for the habitability of other bodies within our Solar Systemand beyond can be assessed. The final goal of astrobiology is to reveal the origin,evolution, and distribution of life on Earth and throughout the Universe in thecontext of cosmic evolution, and thereby to build the foundations for the con-struction and testing of meaningful axioms to support a theory of life.The multidisciplinary character of astrobiology is a challenge on the one hand

because it complies with modern science approaches; on the other hand, the fullexpertise in astrobiology is not always available at a single university. To overcomethis problem, experts from seven different European universities or researchcenters, specialized in leading fields of astrobiology, gathered in an astrobiologylecture course network with live tele-teaching and an interactive question-and-answer period. This book is based mainly on this multidisciplinary lecture series inastrobiology, and each chapter corresponds to a 90-minute lecture. The main fieldsof astrobiology are covered in a very competent and instructive manner.

XV


The book starts with a general introduction to the fascinating world of astro-biology. The next chapters provide insights into the different steps of cosmicevolution, from the Big Bang through the formation of galaxies and stellar systems,with emphasis on the evolution of matter required for life: the elements andmolecules of life. The history of life on Earth is covered in the next chapters,including the latest results about the RNA world and concepts of a “window forlife“ as inferred from life’s strategies to adapt to factually every location on Earth.This leads to a definition of habitability that is applied to the planets and moons ofour Solar System, especially our neighbor planets Venus and Mars and thesatellites of the giant planets, Titan and Europa. With the advent of space explora-tion, space and the bodies of our Solar System are now within our reach; therefore,the technology required for astrobiology missions is also covered, exemplified byastrobiology experiments in low Earth orbit and astrobiology missions to Mars. Thebook concludes with a chapter on the legal and scientific issues of planetaryprotection required for each space mission within our Solar System.This book is intended as a textbook in astrobiology for students and teachers

from various fields of science that are interested in astrobiology. In each chapter, alist of questions for students is included. The CD is based on the original lecturesthat were given at the astrobiology lecture course network. The lectures can befollowed on the Web streaming network of the European Space Agency (ESA)(streamiss.spaceflight.esa.int) under “Astrobiology Lecture Course Network (a.y.2005–2006).”The editors and authors are grateful to the ESA for providing the platform and

support for realizing the Astrobiology Lecture Course Network that this book isbased on. Special thanks go to Daniel Sacotte, Director of Human Spaceflight,Microgravity and Exploration Programmes at ESA for providing continuous sup-port, and to Dieter Isakeit, Massimo Sabbatini, and their staff at the Erasmus UserCentre & Communication Office of ESA for their competent and efficient perform-ance in providing the required video production and infrastructure tools. Thanksgo to former and present coworkers and students of the authors for their contri-butions to the research in the different chapters. Special thanks go to the followingcolleagues or organizations: Frances Westall for collaboration on the postulate forhabitability, which Chapter 6 is based on, and for providing Figure 5.1; BirgitHuber for providing Figure 5.11; L�na Leroy for drawing Figure 3.2; Audrey Nobletfor drawing Figure 3.8; Rainer Facius for providing figures on cosmic radiation inChapter 11; and Gerhard Kminek for valuable comments on the ESA spacemissions and planetary protection for human missions in Chapter 13. Supportfor the laboratory work of Helga Stan Lotter (Chapter 5) by the Austrian FWFgrants P16260 and P18256 is gratefully acknowledged. The PPARC providedfinancial support for the research of Monica Grady (Chapter 8). We appreciatethe encouraging support from Christoph von Friedeburg and Nina Stadthaus fromthe Physics Department of Wiley-VCH, who gave us valuable advice during thepreparation of the book. During the editing process, we had continuous support byFolk Horneck, Lisa Steimel, and Thomas Urlings. Their commitment in reviewing

PrefaceXVI

and proofreading the manuscripts and in reworking electronic versions of thefigures is highly appreciated.

29 June 2006 Gerda HorneckPetra Rettberg

Cologne, Germany

Preface XVII

1Astrobiology: From the Origin of Life on Earthto Life in the UniverseAndr� Brack

This chapter covers the different theories about the steps towardthe origin and evolution of life on Earth, and the major require-ments for these processes and for life at large are discussed.Conclusions are drawn on the likelihood of life originating andpersisting on other places of our Solar System, such as the ter-restrial planets and themoons of the giant planets, or beyond in theUniverse.

1.1General Aspects of Astrobiology

1.1.1Historical Milestones

Humans in every civilization have always been intrigued by their origin and theorigin of life itself. For thousands of years, the comforting theory of spontaneousgeneration seemed to provide an answer to this enduring question. In ancientChina, people thought that aphids were spontaneously generated from bamboos.Sacred documents from India mention the spontaneous formation of flies fromdirt and sweat. Babylonian inscriptions indicate that mud from canals was able togenerate worms.For the Greek philosophers, life was inherent to matter. It was eternal and

appeared spontaneously whenever the conditions were favorable. These ideaswere clearly stated by Thales, Democritus, Epicurus, Lucretius, and even by Plato.Aristotle gathered the different claims into a real theory. This theory safely crossedthe Middle Ages and the Renaissance. Famous thinkers such as Newton, Des-cartes, and Bacon supported the idea of spontaneous generation.The first experimental approach to the question was published in the middle of

the 17th century, when the Flemish physician Van Helmont reported the gener-

1.1 General Aspects of Astrobiology 1


ation of mice from wheat grains and a sweat-stained shirt. He was quite amazed toobserve that they were identical to those obtained by procreation. A controversyarose in 1668, when Redi, a Toscan physician, published a set of experimentsdemonstrating that maggots did not appear when putrefying meat was protectedfrom flies by a thin muslin covering.Six years after Redi’s treatise, the Dutch scientist Anton Van Leeuwenhoek

observed microorganisms for the first time through a microscope that he madehimself. From then on, microorganisms were found everywhere and the support-ers of spontaneous generation took refuge in the microbial world. However, VanLeeuwenhoek was already convinced that the presence of microbes in his solutionswas the result of contamination by ambient air. In 1718, his disciple Louis Joblotdemonstrated that the microorganisms observed in solutions were, indeed,brought in from the ambient air, but he could not convince the naturalists.Even Buffon, in the middle of the 18th century, thought that nature was full of the

germs of life able to scatter during putrefaction and to gather again, later on, toreconstitute microbes. His Welsh friend John Needham undertook many experi-ments to support this view. He heated organic substances in water in a sealed flaskin order to sterilize the solutions. After a while, all solutions showed a profusion ofmicrobes. The Italian priest Lazzaro Spallanzani argued that the sterilization wasincomplete. He heated the solutions to a higher temperature and killed all themicrobes, but he could not kill the idea of microbial spontaneous generation.The controversy reached its apotheosis one century later when Felix Pouchet

published his treatise in 1860. He documented the theory of spontaneous gener-ation in the light of experiments that, in fact, were the results of contamination byambient air. Pasteur gave the finishing blow to spontaneous generation in June1864 when he designed a rigorous experimental set up for sterilization. By usingflasks with long necks that had several bends and were filled with sterilized brothor urine, he showed that no life appeared in the infusions as long as the flaskremained intact.The beautiful demonstration of Pasteur opened the fascinating question of the

historical origin of life. Because life can originate only from preexisting life, it has ahistory and therefore an origin, which must be understood and explained bychemists.Charles Darwin first formulated the modern approach to the chemical origin of

life. In February 1871, he wrote in a private letter to Hooker:

If (and oh, what a big if) we could conceive in some warm littlepond, with all sorts of ammonia and phosphoric salts, light, heat,electricity, etc., present that a protein compound was chemicallyformed, ready to undergo still more complex changes, at the presentday such matter would be instantly devoured or adsorbed, whichwould not have been the case before living creatures were formed.

For 50 years, the idea lay dormant. In 1924, the young Russian biochemistAleksander Oparin pointed out that life must have arisen in the process of theevolution of matter thanks to the nature of the atmosphere, which was considered

1 Astrobiology: From the Origin of Life on Earth to Life in the Universe2

to be reducing. In 1928, the British biologist J. B. S. Haldane, independently ofOparin, speculated on the early conditions suitable for the emergence of life.Subjecting a mixture of water, carbon dioxide, and ammonia to UV light shouldproduce a variety of organic substances, including sugars and some of the materi-als from which proteins are built up. Before the emergence of life they must haveaccumulated in water to form a hot, dilute “primordial soup.” Almost 20 years afterHaldane’s publication, J. D. Bernal conjectured that clay mineral surfaces wereinvolved in the origin of life. In 1953, Stanley Miller, a young student of HaroldUrey, reported the formation of four amino acids – glycine, alanine, aspartic acidand glutamic acid – when he subjected a mixture of methane, ammonia, hydrogen,and water to electric discharges. Miller’s publication really opened the field ofexperimental prebiotic chemistry (see Chapter 3).

1.1.2Searching for Emerging Life

Defining life is a difficult task, and the intriguing and long lasting question “Whatis life?” has not yet received a commonly accepted answer, even for what could bedefined as minimal life, the simplest possible form of life. On the occasion of aWorkshop on Life, held in Modena, Italy, in 2003, each member of the Interna-tional Society for the Study of the Origins of Life was asked to give a definition oflife. The 78 different answers occupy 40 pages in the proceedings of the workshop.Perhaps the most general working definition is that adopted in October 1992 by

the NASA Exobiology Program: “Life is a self-sustained chemical system capable ofundergoing Darwinian evolution.” Implicit in this definition is the fact that thesystem uses external matter and energy provided by the environment. In otherwords, primitive life can be defined, a minima, as an open chemical system capableof self-reproduction, i.e., making more of itself by itself, and capable of evolving.The concept of evolution implies that the chemical system normally transfers itsinformation fairly faithfully but makes a few random errors. These may potentiallylead to higher complexity/efficiency and possibly to better adaptation to changes inthe existing environmental constraints.Schematically, the premises of an emerging life can be compared to parts of

“chemical robots.” By chance, some parts self-assembled to generate robots capableof assembling other parts to form identical robots. Sometimes, a minor error in thebuilding generated more efficient robots, which became the dominant species.In a first approach, present life, based on carbon chemistry in water, is generally

used as a reference to provide guidelines for the study of the origins of life and forthe search for extraterrestrial life. It is generally assumed that the primitive robotsemerged in liquid water and that the parts were already organic molecules. Theearly molecules that contain carbon and hydrogen atoms associated with oxygen,nitrogen, and sulfur atoms are often called the CHONS, where C stands for carbon,H for hydrogen, O for oxygen, N for nitrogen, and S for sulfur.


1.1.3The Role of Water

Liquid water played a major role in the appearance and evolution of life by favoringthe diffusion and exchange of organic molecules. Liquid water has many pecu-liarities. Water molecules establish hydrogen bonds with molecules containinghydrophilic groups. In water, organic molecules containing both hydrophilic andhydrophobic groups self-organize in response to these properties. This dualitygenerates interesting prebiotic situations, such as the stereo-selective aggregationof short peptide sequences of alternating hydrophobic– hydrophilic residues intothermostable �-sheet structures endowed with chemical activity, as shown below.In addition to H-bonding capability, water exhibits a large dipole moment

(1.85 debye) as compared to alcohols (<1.70 debye). This large dipole momentfavors the dissociation of ionizable groups such as -NH2- and -COOH-generatingionic groups, which can form additional H bonds with water molecules, thusimproving their solubility.With a high dielectric constant � of 80, water is an outstanding dielectric

compound. When organic groups with opposite charges Q and Q 0, separated bya distance r, are formed, their recombination is unfavorable because the force ofattraction for reassociation is given by

F ¼ Q �Q 0=�� r2. (1.1).

This is also true for metal ions, which have probably been associated with organicmolecules since the beginning of life.Liquid water was probably active in prebiotic chemistry as a clay producer and

heat dissipator. Further, liquid water is a powerful hydrolytic chemical agent. Assuch, it allows pathways for chemical combinations that would have few chances tooccur in an organic solvent. Liquid water is therefore generally considered as aprerequisite for the emergence of life on Earth.

1.1.4The Physicochemical Features of Carbon-based Life

Life is autocatalytic in essence and is able to evolve. To evolve, i.e., to increase itsdiversity, the molecules bearing the hereditary memory must be able to be ex-tended and diversified by combinatorial dispersive reactions. This can best beachieved with a scaffolding of polyvalent atoms. From a chemical viewpoint, carbonchemistry is by far the most productive in this respect. Another clue in favor ofcarbon is provided by radio astronomers: about 90 carbon-containing moleculeshave been identified in the interstellar medium while only 9 silicon-based mole-cules have been detected (see Chapter 2). To generalize, a carbon-based life is notjust an anthropocentric view, it appears as a highly plausible prerequisite.Carbon atoms exhibit two remarkable features relative to life, one-handedness

and stable isotope distribution. One-handedness, also called homochirality (from


the Greek kheiros, the hand), of the proteins synthesized via the genetic code is acharacteristic of all living systems (see Chapter 3). Each central carbon atom of theamino acid molecule occupies the center of a tetrahedron. Except for the aminoacid glycine, the four substituents of the central carbon atom are different. Thecarbon atom is therefore asymmetrical and it is not superimposable onto its mirrorimage. Each amino acid exists in twomirror-image forms called enantiomers (fromthe Greek enantios, opposed). All protein amino acids have the same handedness:they are homochiral. They are left-handed and hence known as L-amino acids.Their right-handed mirror images are known as D-amino acids. L-amino acidsengaged in a protein chain generate right-handed, single-strand Æ-helices andasymmetrical, multi-strand �-sheet structures. Nucleotides, the building blocksof the nucleic acids DNA and RNA, are also homochiral. Their nomenclature ismore complex because each nucleotide possesses four asymmetrical carbon atoms.In this case, the geometry of a selected carbon atom was chosen. Following thisconvention, nucleotides are right-handed. Right-handed nucleotides generallygenerate right-handed helical nucleic acids.Pasteur was probably the first to realize that biological asymmetry could best

distinguish between inanimate matter and life. Life that would simultaneously useboth right- and left-handed forms of the same biological molecules appears veryunlikely for geometrical reasons. For example, enzyme �-pleated sheets cannotform when both L- and D-amino acids are present in the same molecule. Becausethe catalytic activity of an enzyme is intimately dependent upon the geometry of thechain, the absence of �-pleated sheets would impede, or at least considerablyreduce, the activity spectrum of the enzymes. The use of one-handed biomonomersalso sharpens the sequence information of the biopolymers. For a polymer made ofn units, the number of sequence combinations will be divided by 2 n when thesystem uses only homochiral (one-handed) monomers. Taking into account thefact that enzyme chains are generally made up of hundreds of monomers, and thatnucleic acids contain several million nucleotides, the tremendous gain in simplic-ity offered by the use of monomers restricted to one handedness is self-evident.Finally, if the biopolymers to be replicated were to contain L- and D-units located

at specific sites, the replication process would have to not only be able to positionthe right monomers at the right place but also select the right enantiomer fromamong two species, which differ only by the geometry of the asymmetrical carbonatoms. For example, the bacterium Bacillus brevis is able to synthesize the peptidegramicidin A, which is constructed on a strict alternation of left- and right-handedamino acids. However, the biosynthesis of this peptide involves a set of complexand sophisticated enzymes that are homochiral.Life on Earth uses homochiral left-handed amino acids and right-handed sugars.

A mirror-image life, using right-handed amino acids and left-handed sugars, isperfectly conceivable and might have developed on another planet. Thus, homo-chirality is generally considered a crucial signature for life.The uptake of carbon dioxide by living systems can produce biomolecules

enriched in 12C carbon isotopes at the expense of 13C isotopes. For example, onEarth, over 1600 samples of fossil kerogen (a complex organic macromolecule


produced from the debris of biological matter) have been compared with carbo-nates in the same sedimentary rocks. The organic matter is enriched in 12C byabout 25‰. This offset is now taken to be one of the most powerful indications thatlife on Earth was active nearly 3.9 billion years ago, because the sample suiteencompasses specimens right across the geologic timescale.

1.1.5Clays as Possible Primitive Robots

Any scientist who has observed the crystallization of minerals initiated by theaddition of seeds to a supersaturated solution is tempted to associate life withmineral crystals. Jean Schneider, for example, suggested that complex dislocationnetworks encountered in crystals may, in some cases, follow the criteria of livingunits and lead to a crystalline physiology. He also discussed the places of possibleoccurrence in nature of this kind of physiology, such as terrestrial and extraterres-trial rocks, interplanetary dust, white dwarfs, and neutron stars.According to Cairns-Smith, there is no compelling reason to necessarily relate

the last common ancestor made of organic molecules with first life. Although theeasy accessibility of numerous organic building blocks of life has been demon-strated experimentally, the dominant use of these molecules in living organismscan be seen as a result of evolution rather than a prerequisite for its initiation.Cairns-Smith proposed that the first living systems, and the chemical evolutionpreceding it, might have been based on a chemistry different from that which weknow. The structurally and functionally complex genetic system of modern lifearose subsequently in a living organism using a less efficient primary system witha much higher probability of spontaneous assembly. As genetic candidates, headvocated crystalline inorganic materials presenting suitable properties, such asthe ability to store and replicate information in the form of defaults, dislocations,and substitutions. Clay minerals, such as kaolinite, are particularly attractivebecause they form at ambient temperatures from aqueous weathering of silicaterock.The following “genetic takeover” scenario was proposed by Cairns-Smith as a

mineral origin of life. Certain clays having properties that favor their synthesisproliferated, and their replication defects, likewise, became more common. Incertain clay lineages, the development of crude photochemical machinery favoredthe synthesis of some non-clay species, such as polyphosphates and small organiccompounds. Natural selection favored these lineages of clays because the organiccompounds they produce catalyzed the clay formation. Multiple-step pathways ofhigh specificity, including chiral stereoselection, arose through specific adsorption,followed by the appearance of polymers of specified sequence, at first serving onlystructural roles. Base-paired polynucleotides replicated, giving rise to secondaryand minor genetic material. This secondary material proved to be useful in thealignment of amino acids for polymerization. The ability to produce specificenzymes came concomitantly with the ability to produce sequence-specified poly-peptides and proteins. More-efficient pathways of organic synthesis ensued, and


finally the clay machinery was dispensed with in favor of a polynucleotide-basedreplication–translation system. Although each step of the hypothetical sequence ofevents was developed in detail, the scenario has not been supported by experimen-tal facts.

1.2Reconstructing Life in a Test Tube

It is now a generally accepted conception that life emerged in water and that thefirst self-reproducing molecules and their precursors were probably organic mol-ecules built up with carbon atom skeletons. Organic molecules were formed fromgaseous molecules containing carbon atoms (methane, carbon dioxide, carbonmonoxide), nitrogen atoms (nitrogen, ammonia), or sulfur atoms (hydrogen sul-fide, sulfur oxide). The energy for these reactions came from electric discharges,cosmic and UV radiation, or heat.

1.2.1The Quest for Organic Molecules

1.2.1.1 Terrestrial ProductionIn 1953, Stanley Miller exposed a mixture of methane, ammonia, hydrogen, andwater to electric discharges to mimic the effects of lightning. Among the com-pounds formed, he identified 4 of the 20 naturally occurring amino acids, thebuilding blocks of proteins. Since this historic experiment, 17 natural amino acidshave been obtained via the intermediate formation of simple precursors, such ashydrogen cyanide and formaldehyde. It has been shown that spark dischargesynthesis of amino acids occurs efficiently when a reducing gas mixture containingsignificant amounts of hydrogen is used (see Chapter 3). However, the truecomposition of the primitive Earth atmosphere remains unknown. Today, geo-chemists favor a non-reducing atmosphere dominated by carbon dioxide. Undersuch conditions, the production of amino acids appears to be very limited. Stronglyreducing environments capable of reducing carbon dioxide were necessary for thesynthesis of amino acids.Deep-sea hydrothermal systems may represent suitable reducing environments

for the synthesis of prebiotic organic molecules. The ejected gases contain carbondioxide, carbon monoxide, sulfur dioxide, nitrogen, and hydrogen sulfide. Forinstance, high concentrations of hydrogen (more than 40% of the total gas) andmethane have been detected in the fluids of the Rainbow ultramafic hydrothermalsystem of the Mid-Atlantic Ridge. The production of hydrogen, a highly reducingagent favoring prebiotic syntheses, is associated with the hydrous alteration ofolivine into serpentine and magnetite, a reaction known as “serpentinization.”Indeed, hydrocarbons containing 16 to 29 carbon atoms have been detected inthese hydrothermal fluids. Amino acids have been obtained, although in low yields,under conditions simulating these hydrothermal vents.

1.2 Reconstructing Life in a Test Tube 7

According to W�chtersh�user (1994), primordial organic molecules formed nearthe hydrothermal systems; the energy source required to reduce the carbon dioxidemight have been provided by the oxidative formation of pyrite (FeS2), from ironsulfide (FeS) and hydrogen sulfide (H2S). Pyrite has positive surface charges andbonds the products of carbon dioxide reduction, giving rise to a two-dimensionalreaction system, a “surface metabolism.” Laboratory work has provided support forthis promising new “metabolism-first” approach. Iron sulfide, hydrogen sulfide,and carbon dioxide react under anaerobic conditions to produce hydrogen and aseries of thiols, including methanethiol. Methanethiol and acetic acid have alsobeen obtained from carbon monoxide, hydrogen sulfide, iron and nickel sulfides,and catalytic amounts of selenium. Under specific conditions, thioesters areformed that might have been the metabolic driving force of a “thioester world,”according to de Duve (1998). Thioesters are sulfur-bearing organic compounds thatpresumably would have been present in a sulfur-rich, volcanic environment on theearly Earth.Hydrothermal vents are often disqualified as efficient reactors for the synthesis

of bioorganic molecules because of their high temperature. However, the productsthat are synthesized in hot vents are rapidly quenched in the surrounding coldwater, which may preserve those organics formed.

1.2.1.2 Delivery of Extraterrestrial Organic MoleculesComets and meteorites may have delivered important amounts of organic mole-cules to the primitive Earth (see Chapter 3). Nucleic acid bases, purines, andpyrimidines have been found in the Murchison meteorite. One sugar (dihydroxy-acetone), sugar alcohols (erythritol, ribitol), and sugar acids (ribonic acid, gluconicacid) have been detected in the Murchison meteorite, but ribose, the sugar moietyof ribonucleotides, themselves the building blocks of RNAs (see Chapter 4), has notbeen detected.Eight proteinaceous amino acids have been identified in one such meteorite,

amongmore than 70 amino acids found therein. Cronin and Pizzarello (1997) foundan excess of about 9% of L-enantiomers for some non-protein amino acids detectedin the Murchison meteorite. The presence of L-enantiomeric excesses in thesemeteorites points towards an extraterrestrial process of asymmetric synthesis ofamino acids asymmetry that is preserved inside the meteorite. These excesses mayhelp us to understand the emergence of biological asymmetry or one-handedness.The excess of one-handed amino acids found in the meteorites may result from theprocessing of the organicmantles of the interstellar grains fromwhich themeteoritewas originally formed. That processing could occur, for example, by the effects ofcircularly polarized synchrotron radiation from a neutron star, a remnant of asupernova. On the other hand, strong infrared circular polarization, resultingfromdust scattering in reflection nebulae in theOrionOMC-1 star formation region,has been observed by Bailey. Circular polarization at shorter wavelengthsmight havebeen important in inducing this chiral asymmetry in interstellar organic moleculesthat could be subsequently delivered to the early Earth.


Dust collection in the Greenland and Antarctic ice sheets and its analysis byMaurette show that the Earth captures interplanetary dust as micrometeorites at arate of about 20 000 tons per year. About 99% of this mass is carried by micro-meteorites in the 50–500 �m size range. This value is much higher than the mostreliable estimate of the normal meteorite flux, which is about 10 tons per year. Ahigh percentage of micrometeorites in the 50–100 �m size range have been ob-served to be unmelted, indicating that a significant fraction traversed the terrestrialatmosphere without drastic heating. In this size range, the carbonaceous micro-meteorites represent 20% of the incoming micrometeorites, and they contain 2.5%carbon on average. This flux of incoming micrometeorites might have brought tothe Earth about 2.5 � 1022 g carbon over the period corresponding to the late heavybombardment. As inferred from the lunar craters, during this period planetesimals,asteroids, and comets impacted the Earth until about 3.85 billion years ago (seeChapter 2). For comparison, this delivery represents more carbon than is in thepresent surficial biomass, which amounts to about 1018 g. In addition to organiccompounds, these grains contain a high proportion of metallic sulfides, oxides, andclay minerals that belong to various classes of catalysts. In addition to the carbona-ceous matter, micrometeorites might also have delivered a rich variety of catalysts.These may have functioned as tiny chemical reactors when reaching oceanic water.On 15 January 2006, the Stardust reentry probe brought cometary grains to the

Earth for the first time. The preliminary analyses of these grains from comet Wild-2 confirmed that micrometeorites are probably witnesses of a chemical continuum– via the cometary grains – from the interstellar medium, where they form, toterrestrial oceans. Comets are the richest planetary objects in organic compoundsknown so far. Ground-based observations have detected hydrogen cyanide andformaldehyde in the coma of comets.In 1986, onboard analyses performed by the two Russian missions Vega 1 and

Vega 2, as well as observations obtained by the European mission Giotto and thetwo Japanese missions Suisei and Sakigake, demonstrated that Halley’s Cometshows substantial amounts of organic material. On average, dust particles ejectedfrom Halley’s nucleus contain 14% organic carbon by mass. About 30% ofcometary grains were dominated by the light elements C, H, O, and N, and 35%are close in composition to the carbon-rich meteorites. The presence of organicmolecules, such as purines, pyrimidines, and formaldehyde polymers, has beeninferred from the fragments analyzed by the Giotto PICCA and Vega PUMA massspectrometers. However, there was no direct identification of the complex organicmolecules probably present in the cosmic dust grains and in the cometary nucleus.Many chemical species of interest for exobiology were detected in Comet Hya-

kutake in 1996, including ammonia, methane, acetylene (ethyne), acetonitrile(methyl cyanide), and hydrogen isocyanide. The study of the Hale-Bopp Cometin 1997 led to the detection of methane, acetylene, formic acid, acetonitrile, hydro-gen isocyanide, isocyanic acid, cyanoacetylene, formamide, and thioformaldehyde.It is possible, therefore, that cometary grains might have been an important

source of organic molecules delivered to the primitive Earth. Comets orbit onunstable trajectories and sometimes collide with planets. The collision of Comet


Shoemaker-Levy 9 with Jupiter in July 1994 is a recent example of such an event.Such collisions were probably more frequent 4 billion years ago, when the cometsorbiting around the Sun were more numerous than today. By impacting the Earth,comets probably delivered a substantial fraction of the terrestrial water (about 35%according to the estimation of Owen based on the relative contents in hydrogen anddeuterium) in addition to organic molecules. The chemistry that is active at thesurface of a comet is still poorly understood. The European mission Rosetta,launched in 2004, will analyze the nucleus of the comet 67 P/Churyumov-Ger-asimenko. The spacecraft will first study the environment of the comet during aflyby over several months, and then a probe will land to analyze the surface and thesubsurface ice sampled by drilling.

1.2.2Space Experiments

Ultraviolet (UV) irradiation of dust grains in the interstellar medium may result inthe formation of complex organic molecules. The interstellar dust particles areassumed to be composed of silicate grains surrounded by ices of different mole-cules, including carbon-containing molecules (see Chapter 3). In a laboratoryexperiment, ices of H2O, CO2, CO, CH3OH, and NH3 were deposited at 12 K undera pressure of 10–5 Pa (10–7 mbar) and were then irradiated by electromagneticradiation representative of that in the interstellar medium. The solid layer thatdeveloped on the solid surface was analyzed by enantioselective gas chromatog-raphy coupled with mass spectrometry (GC-MS). After the analytical steps ofextraction, hydrolysis, and derivatization, 16 amino acids were identified in thesimulated ice mantle of interstellar dust particles. These experiments confirmedthe preliminary amino acid formation obtained first by Greenberg. The chiralamino acids were identified as being totally racemic (consisting of equal amountsof D- and L-enantiomers). Parallel experiments performed with 13C-containingsubstitutes definitely excluded contamination by biological amino acids. Theresults strongly suggest that amino acids are readily formed in interstellar space.Before reaching the Earth, organic molecules are exposed to UV radiation, both

in interstellar space and in the Solar System. Amino acids have been exposed inEarth orbit to study their survival in space. The UV flux of wavelengths <206 nm inthe diffuse interstellar medium is about 108 photons cm–2 s–1. In Earth orbit, thecorresponding solar flux is in the range of 1016 photons cm–2 s–1. This means thatan irradiation over one week in Earth orbit corresponds to that over 275 000 years inthe interstellar medium. Thin films of amino acids, like those detected in theMurchison meteorite, have been exposed to space conditions in Earth orbit withinthe BIOPAN facility of the European Space Agency (ESA) onboard the unmannedRussian satellites Foton 8 and Foton 11 (see Chapter 11). Aspartic acid and glutamicacid were partially destroyed during exposure to solar UV. However, decomposi-tion was prevented when the amino acids were embedded in clays.Amino acids and peptides have also been subjected to solar radiation outside the

MIR station for 97 days. After three months of exposure, about 50% of the amino


acids were destroyed in the absence of mineral shielding. Peptides exhibited anoticeable sensitivity to space vacuum, and sublimation effects were detected.Decarboxylation was found to be the main effect of photolysis. No polymerizationoccurred and no racemization (the conversion of L- or D-amino acids into a racemicmixture) was observed. Some samples were embedded into mineral material(montmorillonite clay, basalt, or Allendemeteorite) when exposed to space. Amongthe different minerals, the meteoritic powder offered the best protection, whereasthe clay montmorillonite was the least efficient. Different thicknesses of meteoritepowder films were used to estimate the shielding threshold. Significant protectionfrom solar UV radiation was observed when the thickness of the meteorite mineralwas 5 �m or greater.

1.2.3Attempts to Recreate Life in a Test Tube

By analogy with contemporary living systems, it was long considered that primitivelife emerged as cellular entities, requiring boundary molecules able to isolate thesystem from the aqueous environment (membrane). Further, catalytic moleculeswould be needed to provide the basic chemical work of the cell (enzymes), as well asinformation-retaining molecules that allow the storage and transfer of the infor-mation needed for replication (RNA).Fatty acids are known to form vesicles when the hydrocarbon chains containmore

than 10 carbon atoms. Such vesicle-forming fatty acids have been identified in theMurchison meteorite by Deamer (1985). However, the membranes obtained withthese simple amphiphiles are not stable over a broad range of conditions. Stableneutral lipids can be obtained by condensing fatty acids with glycerol or with glycerolphosphate, thus mimicking the stable contemporary phospholipid. Primitive mem-branes also could initially have been formed by simple isoprene derivatives.Most of the catalytic chemical reactions in a living cell are achieved by proteina-

ceous enzymes made of 20 different homochiral L-amino acids. Amino acids weremost likely available on the primitive Earth as complex mixtures, but the formationof mini-proteins from the monomers in water is not energetically favored. Becausethe peptide bond of proteins is thermodynamically unstable in water, it requires anenergy source, such as heat or condensing chemicals, to link two amino acidstogether in an aqueous milieu. Oligoglycines up to the octamer have been obtainedfrom glycine in a flow reactor simulating hydrothermal circulation. These com-pounds were formed by repeatedly circulating solutions of glycine and CuCl2 froma high-pressure, high-temperature chamber to a high-pressure, low-temperaturechamber, simulating conditions in a hydrothermal vent. Clays and salts may alsobe used to condense free amino acids in water. When subjecting mixtures ofglycine and kaolinite to wet–dry cycles and 25–94 �C temperature fluctuations,the formation of oligopeptides up to five glycines long has been observed.Bulk thermal condensation of amino acids has been described by Fox, who has

shown that dry mixtures of amino acids polymerize when heated to 130�C to give“proteinoids.” In the presence of polyphosphates, the temperature can be decreased


to 60�C. High molecular weights were obtained when an excess of acidic or basicamino acids was present. In aqueous solutions, the proteinoids aggregated sponta-neously to form microspheres of 1–2 �m, presenting an interface resembling thelipid bilayers of living cells. The microspheres increased slowly in size from dis-solved proteinoids and were sometimes able to bud and to divide. These micro-spheres were described as catalyzing the decomposition of glucose and were able towork as esterases and peroxidases. The main advantage of proteinoids is theirorganization into particles, but they also represent a dramatic increase in complexity.The number of condensing agents capable of assembling amino acids into

peptides in water is limited, especially when looking for prebiotically plausiblecompounds. Carbodiimides, having a general formula R-N=C=N-R', power theligation of both glutamic and aspartic acids on hydroxyapatite. The simplestcarbodiimide, H-N=C=N-H, can be considered a transposed form of cyanamide(NH2-CN), which is present in the interstellar medium. In water, cyanamide formsa dimer, dicyandiamide, which is as active as carbodiimides in forming peptides.However, the reactions are very slow and do not proceed beyond the tetrapeptide.Oligomers of glutamic acid greater than 45 amino acids in length were formed

on hydroxyapatite and illite after 50 feedings with glutamic acid and the condens-ing agent carbonyldiimidazole (Im-CO-Im). Amino acid adenylate anhydrides havebeen reported to condense readily in the presence of montmorillonite. According tode Duve (1998), the first peptides may have appeared via thioesters, which generateshort peptides in the presence of mineral surfaces. Among the most effectiveactivated amino acid derivatives for the formation of oligopeptides in aqueoussolution are the N-carboxyanhydrides.Chemical reactions capable of selectively condensing protein amino acids more

readily than non-protein ones have been described. Helical and sheet structuresmay be modeled with the aid of only two different amino acids, the first one beinghydrophobic and the second hydrophilic. Polypeptides with alternating hydro-phobic and hydrophilic residues adopt a water-soluble �-sheet geometry becauseof hydrophobic side-chain clustering. Because of the formation of �-sheets, alter-nating sequences display a good resistance toward chemical degradation. Aggre-gation of alternating sequences into �-sheets is possible only with homochiral (allL or all D) polypeptides, as demonstrated by this author at the Centre de Bio-physique Mol�culaire in Orl�ans, France. Short peptides have also been found toexhibit catalytic properties.In contemporary living systems, the hereditary memory is stored in nucleic acids

built up with bases (purine and pyrimidine), sugars (ribose for RNA, deoxyribosefor DNA), and phosphate groups. The accumulation of significant quantities ofnatural RNA nucleotides does not appear to be a plausible chemical event on theprimitive Earth. Purines are easily obtained from hydrogen cyanide or by subject-ing reduced gas mixtures to electric discharges. No successful pyrimidine synthesisfrom electrical discharges has been published so far, whereas hydrogen cyanideaffords only very small amounts of these bases. Condensation of formaldehydeleads to ribose as well as a large number of other sugars. Although the synthesis ofpurine nucleosides (the combination of purine and ribose) and of nucleotides has


been achieved by heating the components in the solid state, the yields are very lowand the reactions are not regioselective. Interestingly, very effective montmorillon-ite-catalyzed condensation of nucleotides into oligomers up to 55 monomers longhas been reported by Ferris from nucleoside phosphorimidazolides.The synthesis of oligonucleotides is much more efficient in the presence of a

preformed, pyrimidine-rich polynucleotide acting as a template. Non-enzymaticreplication has been demonstrated by Orgel. The preformed chains align thenucleotides by base-pairing to form helical structures that bring the reactinggroups into close proximity. However, the prebiotic synthesis of the first oligonu-cleotide chains remains an unsolved challenge.

1.2.4A Primitive Life Simpler than a Cell?

Thomas Cech found that some RNAs, the ribozymes, have catalytic properties (seeChapter 4). For example, they increase the rate of hydrolysis of oligoribonucleotides.They also act as polymerization templates, because chains up to 30 monomers longcan be obtained starting from a pentanucleotide. Since this primary discovery, thecatalytic spectrumof these ribozymes has been considerably enlarged by the directedtest tube molecular evolution experiments initiated in the laboratories of GeraldJoyce and Jack Szostak. Since RNA was shown to be able to act simultaneously asgeneticmaterial and as a catalyst, RNAhas been considered the first living systemonthe primitive Earth (the “RNA world”). This is because it can simultaneously be thegenotype and the phenotype and can fulfill the basic cycle of life consisting of self-replication, mutation, and selection. Strong evidence for this proposal has beenobtained from the discovery that modern protein synthesis in the ribosome iscatalyzed by RNA. One should, however, remember that RNAs synthesis underprebiotic conditions remains an unsolved challenge. It seems unlikely that lifestarted with RNA molecules, because these molecules are not simple enough. TheRNA world appears to have been an episode in the evolution of life before theappearance of cellular microbes rather than the spontaneous birth of life.RNA analogues and surrogates have been studied. The initial proposal was that

the first RNA was a flexible, achiral derivative in which ribose was replaced byglycerol, but these derivatives did not polymerize under prebiotic conditions. Theease of forming pyrophosphate (double phosphate) bonds prompted investigationof linking nucleotides by pyrophosphate groups. This proposal was tested using thereactions of the diphosphorimidazolides of deoxynucleotides. Their reaction in thepresence of magnesium or manganese ions resulted in the formation of 10–20mers of the oligomers.Considering the ease of formation of hexose-2,4,6-triphosphates from glycolal-

dehyde phosphate in a process analogous to the formose reaction, Eschenmoserand coworkers chemically synthesized polynucleotides containing hexopyranoseribose (pyranosyl-RNA or p-RNA) in place of the usual “natural” pentofuranoseribose found in RNA. p-RNAs form Watson-Crick-paired double helices that aremore stable than RNA. Furthermore, the helices have only a weak twist, which


should make it easier to separate strands during replication. Replication experi-ments have had marked success in terms of sequence copying but have failed todemonstrate template-catalysis turnover numbers greater than 1. The chemicalsynthesis of threo furanosyl nucleic acid (TNA), an RNA analogue built on thefuranosyl form of the tetrose sugar threose, was also reported by the Eschenmosergroup. TNA strands are much more stable in aqueous solution than RNA and areresistant to hydrolysis. They form complementary duplexes between complemen-tary strands. Moreover, of even greater potential importance, they form comple-mentary strands with RNA. This raises the possibility that TNAs could have servedas templates for the formation of complementary RNAs by template-directedsynthesis. TNA is a more promising precursor to RNA than p-RNA, becausetetroses have the potential to be synthesized from glycolaldehyde phosphate andtwo other carbon precursors, which may have been present in quantities greaterthan those of ribose on the primitive Earth.Peptide nucleic acids (PNA), first synthesized by Nielsen and coworkers, consist

of a peptide-like backbone to which nucleic acid bases are attached. PNAs form verystable double-helical structures with complementary strands of PNA (PNA-PNA),DNA (PNA-DNA), RNA (PNA-RNA), and even stable PNA2-DNA triple helices.Information can be transferred from PNA to RNA, and vice versa, in template-directed reactions. Although PNA hydrolyzes rather rapidly, thus considerablyrestricting the chances of PNA ever having accumulated in the primitive terrestrialoceans, the PNA-PNA double helix illustrates that genetic information can bestored in a broad range of double-helical structures.Chemists are also tempted to consider that primitive self-replicating systems

must have used simpler informational molecules than biological nucleic acids ortheir analogues. Because self-replication is, by definition, autocatalysis, they aresearching for simple autocatalytic molecules capable of mutation and selection.Reza Ghadiri tested peptides as possible templates, and non-biological organicmolecules have been screened by G�nter von Kiedrowski. In most cases, the rate ofthe autocatalytic growth was not linear. The initial rate of autocatalytic synthesiswas found to be proportional to the square root of the template concentration: thereaction order in these autocatalytic self-replicating systems was found to be 1/2rather than 1, a limiting factor as compared to most autocatalytic reactions knownso far. Autocatalytic reactions are particularly attractive because they might amplifysmall enantiomeric excesses, eventually extraterrestrial, to homochirality.

1.3The Search for Traces of Primitive Life

1.3.1Microfossils

The first descriptions of fossil microorganisms in the oldest, well-preserved sedi-ments (3.5–3.3 billion years old) from Australia and South Africa were made by


William Schopf and Elso Barghoorn. Although their observations have been calledinto question, Westall and others have more recently established that life wasabundant in these rocks. From a theoretical point of view, the earliest forms of lifewould most likely have had a chemolithoautotrophic metabolism, using inorganicmaterials as a source of both carbon and energy. Evidence for the presence ofchemolithotrophs in the hydrothermal deposits from Barberton and the Pilbaracomes from the N and C isotopic data. Considering the high temperatures on theearly Earth, it is probable that the earliest microorganisms were thermophilic.Structures resembling oxygenic photosynthetic microorganisms such as cyanobac-teria have been described, and carbon isotope data have been interpreted asevidence for their presence. However, these interpretations are strongly disputed.Nevertheless, the fact that the microorganisms inhabiting the early Archeanenvironments of Barberton (South Africa) and Pilbara (Australia) formed matsin the photic zone suggests that some of them may already have developedanoxygenic photosynthesis.

1.3.2Oldest Sedimentary Rocks

The oldest sedimentary rocks occur in southwest Greenland and have been dated at3.8–3.85 billion years by Manfred Schidlowski and Stephen Mozsis. The old sedi-ments testify to the presence of permanent liquid water on the surface of the Earthand to the presence of carbon dioxide in the atmosphere. They contain organiccarbon. Minik Rosing found that the isotopic signatures of the organic carbonfound in Greenland meta-sediments provide indirect evidence that life may be 3.85billion years old. Taking the age of the Earth as about 4.6 billion years, this meansthat life must have begun quite early in Earth’s history. Although there are seriousreservations concerning these studies (contamination by more recent fossilizedendoliths, 12C enrichment produced by thermal decomposition of siderite andmetamorphic processes), stepped combustion analysis by Mark von Zuilen hasverified the existence of the 12C enrichment in these sediments.

1.4The Search for Life in the Solar System

1.4.1Planet Mars and the SNC Meteorites

The mapping of Mars by the spacecrafts Mariner 9, Viking 1 and Viking 2, MarsGlobal Surveyor, and Mars Express revealed channels and canyons resembling dryriverbeds (see Chapter 8). The gamma-ray spectrometer instrument onboard theMars orbiter Odyssey detected hydrogen, which indicates the presence of water icein the upper meter of soil in a large region surrounding the planet’s south pole,where ice is expected to be stable. The amount of hydrogen detected indicates 20–

1.4 The Search for Life in the Solar System 15

50% ice by mass in the lower layer beneath the topmost surface. The ice-rich layeris about 60 cm beneath the surface at latitude 60 ºS and approaches 30 cm of thesurface at latitude 75 ºS. The ancient presence of liquid water on the surface ofMars was confirmed by the two AmericanMars Exploration Rovers (MER A and B),Spirit and Opportunity, and by the presence of sulfates and clays revealed by theinfrared spectrometer OMEGA onboard the European Mars orbiter Mars Express.However, Martian oceans were probably restricted to the very early stages ofMartian history. Mars therefore possessed an atmosphere capable of deceleratingcarbonaceous micrometeorites, and chemical evolution may have been possible onthe planet.The Viking 1 and Viking 2 lander missions were designed to address the question

of extant (rather than extinct) life on Mars (see Chapter 5). Three experiments wereselected to detect metabolic activity, such as photosynthesis, nutrition, and respi-ration of potential microbial soil communities. The results were ambiguous,because although “positive” results were obtained, no organic carbon was foundin the Martian soil by gas chromatography–mass spectrometry (GC-MS). It wasconcluded that the most plausible explanation for these results was the presence atthe Martian surface of highly reactive oxidants, such as hydrogen peroxide, whichwould have been photochemically produced in the atmosphere. Direct photolyticprocesses were suggested to be responsible for the degradation of organics at theMartian surface. Because the Viking landers could not sample soils below 6 cm, thedepth of this apparently organic-free and oxidizing layer is still unknown. Moreinformation is expected from the upcoming lander missions to Mars: the U. S.Mars Science Laboratory (MSL) to be launched in 2009 and the European ExoMarsmission to be launched in 2013 (see Chapter 12).There are Martian rocks on Earth represented by a small group of meteorites of

igneous (volcanic) origin, known as the SNCmeteorites (after their type specimensShergotty, Nakhla, and Chassigny), that had comparatively young crystallizationages, equal to or less than 1.3 billion years (see Chapter 8). One of these meteorites,designated EETA79001, was found in Antarctica in 1979. It had gas inclusionstrapped within a glassy component. Both compositionally and isotopically, this gasmatched the makeup of the Martian atmosphere, as measured by the Viking massspectrometer. The data provide a very strong argument that at least that particularSNC meteorite came from Mars, representing the product of a high-energy impactthat ejected material into space. There are now 34 SNC meteorites known in total.Two of the SNC meteorites, EETA79001 and ALH84001, supply new and highly

interesting information. A subsample of EETA79001, excavated from deep withinthe meteorite, has been subjected to stepped combustion. The CO2 release from200–400�C suggested the presence of organic molecules. The carbon is enriched in12C, and the carbon isotope difference between the organic matter and the carbo-nates in Martian meteorites is greater than that observed on Earth. This could beindicative of biosynthesis, although some as yet unknown abiotic processes couldperhaps explain this enrichment. David McKay has reported the presence of otherfeatures in ALH84001 that may represent a signature of relic biogenic activity onMars, but this biological interpretation is strongly questioned.


Because Mars had a presumably “warm” and wet past climate, it should havesedimentary rocks deposited by running and/or still water on its surface as well aslayers of regolith generated by impacts. Such consolidated sedimentary rockstherefore ought to be found among the Martian meteorites. However, no suchsedimentary material has been found in any SNCmeteorite. It is possible that theydid survive the effects of the escape acceleration from the Martian surface but didnot survive terrestrial atmospheric entry because of decrepitation of the cementingmineral. The “STONE” experiment, flown by ESA, was designed to study preciselysuch physical and chemical modifications to sedimentary rocks during atmospher-ic entry from space (see Chapter 11). A piece of basalt (representing a standardmeteoritic material), a piece of dolomite (sedimentary rock), and an artificialMartian regolith material (80% crushed basalt and 20% gypsum) were embeddedinto the ablative heat shield of the satellite Foton 12, which was launched on 9September 1999 and landed on 24 September 1999. Such an experiment had neverbeen performed before, and the samples, after their return, were analyzed for theirchemistry, mineralogy, and isotopic compositions by a European consortium.Atmospheric entry modifications are made visible by reference to the untreatedsamples. The results suggest that some Martian sedimentary rocks might, in part,survive terrestrial atmospheric entry from space.Even if convincing evidence for ancient life in ALH84001 has not been estab-

lished, the two SNCmeteorites (EETA79001 and ALH84001) do show the presenceof organic molecules. This suggests that the ingredients required for the emer-gence of primitive life were present on the surface of Mars. Therefore, it istempting to consider that microorganisms may have developed on Mars and livedat the surface until liquid water disappeared. Because Mars probably had no platetectonics, and because liquid water seems to have disappeared from Mars’ surfacevery early, theMartian subsurface perhaps keeps a frozen record of very early formsof life.Currently, a very intensive exploration of Mars is planned, and U. S., European,

Russian, and Japanese missions to Mars are taking place or are in the planning.Exobiology interests are included, especially in the analysis of samples from siteswhere the environmental conditions may have been favorable for the preservationof evidence of possible prebiotic or biotic processes. The European Space Agency(ESA) convened an Exobiology Science Team chaired by this author to design anintegrated suite of instruments to search for evidence of life on Mars. Priority wasgiven to the in situ organic and isotopic analysis of samples obtained by subsurfacedrilling. The basic recommendations of the Exobiology Science Team are presentlyserving as guidelines for the elaboration of the Pasteur exobiology payload of theESA ExoMars mission scheduled for 2013 (see Chapter 12).

1.4.2Jupiter’s Moon Europa

The Jovian moon Europa appears as one of the most enigmatic of the Galileansatellites. With a mean density of about 3.0 g cm–3, the Jovian satellite should be

1.4 The Search for Life in the Solar System 17

dominated by rocks. Ground-based spectroscopy, combined with gravity data,suggests that the satellite has an icy crust, which is kilometers thick, and a rockyinterior. The images obtained by the Voyager spacecraft in 1979 showed very fewimpact craters on Europa’s surface, indicating recent, and probably continuing,resurfacing by cryovolcanic and tectonic processes. Recent images of Europa’ssurface, taken by the Galileo spacecraft over 14 months (from December 1997 toDecember 1999), show surface features – iceberg-like rafted blocks, cracks, ridges,and dark bands – that are consistent with the presence of liquid water beneath theicy crust. Data from Galileo’s near-infrared mapping spectrometer show hydratedsalts that could be evaporites. The most convincing argument for the presence ofan ocean of liquid water comes from Galileo’s magnetometer. The instrumentdetected an induced magnetic field within Jupiter’s strong magnetic field. Thestrength and response of the induced field require a near-surface, global conduct-ing layer, most likely a layer of salty water (see Chapter 10).If liquid water is present within Jupiter’s moon Europa, it is quite possible that it

includes organic matter derived from thermal vents. Terrestrial-like prebioticorganic chemistry and primitive life may therefore have developed in Europa’socean. If Europa maintained tidal and/or hydrothermal activity in its subsurfaceuntil now, it is possible that microbial activity is still present. Thus, the possibilityof extraterrestrial life present in a subsurface ocean of Europa must seriously beconsidered. The most likely sites for extant life would be at hydrothermal ventsbelow the most recently resurfaced area. To study this directly would requiremaking a borehole through the ice in order to deploy a robotic submersible. Onthe other hand, biological processes in and around hydrothermal vents couldproduce biomarkers that would be pushed up as traces in cryovolcanic eruptionsand thereby be available at the surface for in situ analysis or sample return. Mineralnutrients delivered through cryovolcanic eruption would make the same locationsthe best candidates for autotrophic life.

1.4.3Saturn’s Moon Titan

Titan’s atmosphere was revealed mainly by the Voyager 1 mission in 1980, whichyielded the bulk composition (90% molecular nitrogen and about 1–8% methane).Also, a great number of trace constituents were observed in the form of hydro-carbons, nitriles, and oxygen-containing compounds, mostly CO and CO2. Titan isthe only other object in our Solar System bearing any resemblance to our own planetin terms of atmospheric pressure, which amounts to 1.5 105 Pa (1.5 bar), andcarbon/nitrogen chemistry. It therefore represents a natural laboratory for studyingthe formation of complex organic molecules on a planetary scale and over geologicaltimes (see Chapter 9). The European Space Agency’s Infrared Space Observatory(ISO) has detected tiny amounts of water vapor in the higher atmosphere, but Titan’ssurface temperature (94 K) is much too low to allow the presence of liquid water.Although liquid water is totally absent at the surface, the satellite provides a uniquemilieu to study, in situ, the products of the fundamental physical and chemical


interactions driving a planetary organic chemistry. Herewith, Titan serves as areference laboratory to study, by default, the role of liquid water in exobiology.The NASA–ESA Cassini–Huygens spacecraft launched in October 1997 arrived in

the vicinity of Saturn in 2004 and performed several flybys of Titan, makingspectroscopic, imaging, radar, and other measurements. On 14 January 2005, aninstrumented descent probe managed by European scientists penetrated the at-mosphere and systematically studied the organic chemistry in Titan’s geofluid. For150 min, in situmeasurements provided analyses of the organics present in the air,in the aerosols, and at the surface. The GC-MS of theHuygens probe measured thechemical composition and the isotopic abundances, from an altitude of 140 kmdown to the surface. The main findings are as follows:

• nitrogen and methane are the main constituents of theatmosphere;

• the isotopic ratio 12C/13C suggests a permanent supply ofmethane in the atmosphere;

• the surface is “wetted” by liquid methane and rich in organics(cyanogen, ethane);

• the presence of 40Ar suggests the existence of internalgeological activity.

1.5The Search for Life Beyond the Solar System

1.5.1The Search for Rocky Earthlike Exoplanets

Apart from abundant hydrogen and helium, 114 interstellar and circumstellargaseous molecules have been identified in the interstellar medium (see Chapter 2).It is commonly agreed that the catalog of interstellar molecules represents only afraction of the total spectrum of molecules present in space, the spectral detectionbeing biased by the fact that only those molecules possessing a strong electricdipole can be observed. Among these molecules, 83 contain carbon, whereas only 7contain silicon. Silicon has been proposed as an alternative to carbon as the basis oflife. However, silicon chemistry is apparently less inventive and does not seem tobe able to generate any life as sophisticated as the terrestrial carbon-based one. Maythese molecules survive the violent accretion phase generating a planetary system?The origin and distribution of the molecules from the interstellar medium to the

planets, asteroids, and comets of the Solar System are presently at the center of adebate based on isotope ratios. Some molecules might have survived in coldregions of the outer Solar System, whereas others would have been totally reproc-essed during accretion. Whatever the case, the interstellar medium tells us thatorganic chemistry is universal.What about liquid water? New planets have been discovered beyond the Solar

System. On 6 October 1995, the discovery of an extrasolar planet, i.e., a planet

1.5 The Search for Life Beyond the Solar System 19

outside our Solar System, was announced byMichel Mayor and Didier Queloz. Theplanet orbits an 8 billion year old star called 51 Pegasus, 42 light years away withinthe Milky Way. The suspected planet takes just four days to orbit 51 Pegasus. It hasa surface temperature around 1000�C and a mass about 0.5 the mass of Jupiter.One year later, seven other extrasolar planets were identified. Among them, 47Ursa Major has a planet with a surface temperature estimated to be around that ofMars (–90 to –20 �C), and the 70 Virginis planet has a surface temperatureestimated at about 70–160 �C. The latter is the first known extrasolar planet whosetemperature might allow the presence of liquid water. As of May 2006, 193exoplanets had been observed.

1.5.2Detecting Extrasolar Life

Extrasolar life, i.e., life on a planet of a solar system other than our own, will not beaccessible to space missions in the foreseeable future. The formidable challenge ofdetecting distant life must therefore be tackled by astronomers and radio astron-omers. The simultaneous detection of water, carbon dioxide, and ozone (an easilydetectable telltale signature of oxygen) in the atmosphere would constitute themost convincing biomarker but not absolute proof. Other anomalies in the atmos-pheres of telluric exoplanets (i.e., rocky Earthlike planets), such as the presence ofmethane, might be the signature of an extrasolar life. European astrophysicists areproposing the construction of a flotilla of four free-flying spacecrafts, each con-taining an infrared telescope of 3 m in diameter, to search for signs of life onterrestrial-like planets. The mission, called Darwin-IRSI, is presently under studyat ESA. Finally, the detection of an unambiguous electromagnetic signal (via theSearch for Extraterrestrial Intelligence program) would obviously be an excitingevent.

1.6Conclusions

On Earth, life probably appeared about 4 billion years ago, when some assemblagesof organic molecules in a liquid water medium began to transfer their chemicalinformation and to evolve by making a few accidental transfer errors. The numberof molecules required for those first assemblages is still unknown. The problem isthat on Earth, those molecules have been erased. If life started on Earth with theself-organization of a relatively small number of molecules, its emergence musthave been fast; therefore, the chance of the appearance of life on any appropriatecelestial bodies might be real. On the other hand, if the process required thousandsof different molecules, the event risks being unique and restricted to the Earth.The discovery of a second independent genesis of life on a body presenting

environmental conditions similar to those prevailing on the primitive Earth wouldstrongly support the idea of a rather simple genesis of terrestrial life. More than


just a societal wish, the discovery of a second genesis of life is a scientific need forthe study of the origin of life. It will demonstrate that life is not a magic, one-shotprocess but a rather common phenomenon. Many scientists are convinced thatmicrobial life is not restricted to the Earth, but such conviction now needs to besupported by facts.

1.7Further Reading

1.7.1Books and Articles in Books

Brack, A. (Ed.) The Molecular Origins of Life:Assembling Pieces of the Puzzle, CambridgeUniversity Press, Cambridge, 1998.

Gilmour, I., Sephton, M. A. (Eds.) An Intro-duction to Astrobiology, The Open Universityand Cambridge University Press, Cam-bridge, 2003.

Clancy, P., Brack, A., Horneck, G. Looking forLife. Searching the Solar System, CambridgeUniversity Press, Cambridge, 2005.

De Duve, C. Possible starts for primitive life.Clues from present-day biology: the thioest-er world, in: A. Brack (Ed.) The MolecularOrigins of Life: Assembling Pieces of the Puzzle,Cambridge University Press, Cambridge,pp. 219–236, 1998.

Fox, S.W. Dose, K. Molecular Evolution and theOrigin of Life (Revised Edition), MarcelDekker, New York, 1977.

Gargaud, M., Barbier, B., Martin, H., J. Reisse,J. (Eds.) Lectures in Astrobiology, Springer-Verlag, Berlin, Heidelberg, 2005.

Horneck. G., Baumstark-Khan, C. (Eds.)Astrobiology – The Quest for the Conditions ofLife, Springer, Berlin, Heidelberg, NewYork, 2002.

Jakosky, B. The Search for Life on Other Planets,Cambridge University Press, 1998.

Jones, B.W. (Ed.) Life in the Solar System andbeyond, Springer, Berlin, Heidelberg, NewYork 2004.

Maurette, M. Micrometeorites and the Mysteriesof our Origins, Springer, Berlin Heidelberg,New York, 2006.

Rauchfuss, H. Chemische Evolution, Springer,Berlin, Heidelberg, New York, 2005

Schulze-Makuch, D., Irwin L. N. Life in theUniverse, Springer, Berlin, Heidelberg, NewYork, 2004.

Westall, F., Southam, G. The early record oflife, in: K. Benn, J.-C. Mareschal, K. C.Condie (Eds.) Archean Geodynamics and En-vironments, American Geophysical Union,Washington DC, pp. 283–304, 2006.

1.7 Further Reading 21

1.7.2Articles in Journals

Boillot, F., Chabin, A., Bur�, C., Venet, M.,Belsky, A., Bertrand-Urbaniak, M., Delmas,A., Brack, A., Barbier, B. The Perseus exo-biology mission on MIR: behaviour of ami-no acids and peptides in Earth orbit, OriginsLife Evol. Biosphere 2002, 32, 359–385.

Brack, A. From amino acids to prebiotic activepeptides: a chemical reconstitution, PureAppl. Chem. 1993, 65, 1143–1151.

Brack, A., Baglioni, P., Borruat, G., Brandst�t-ter, F., Demets, R., Edwards, H. G.M.,Genge, M., Kurat, G., Miller, M. F., Newton,E.M., Pillinger, C. T., Roten, C.-A., W�sch,E. Do meteoroids of sedimentary originsurvive terrestrial atmospheric entry? TheESA artificial meteorite experiment STONE,Planet. Space Sci. 2002, 50, 763–772.

Cronin, J. R., Pizzarello, S. Enantiomeric ex-cesses in meteoritic amino acids, Science1997, 275, 951–955.

Deamer, D.W. Boundary structures areformed by organic components of theMurchison carbonaceous chondrite, Nature1985, 317, 792–794.

Eschenmoser, A. Chemical etiology of nucleicacid structure, Science 1999, 284, 2118–2124.

Ferris, J. P., Hill, A. R. Jr, Liu, R., Orgel, L. E.Synthesis of long prebiotic oligomers onmineral surfaces, Nature 1996, 381, 59–61.

Luther, A., Brandsch, R., von Kiedrowski, G.Surface-promoted replication and exponen-tial amplification of DNA analogues, Nature1998, 396, 245–248.

Maurette, M., Duprat, J., Engrand, C., Gou-nelle, M., Kurat, G., Matrajt, G., Toppani, A.Accretion of neon, organics, CO2, nitrogenand water rom large interplanetary dustparticles on the early, Earth Planet. Space Sci.2000, 48, 1117–1137.

Mayor, M. D., Queloz, D. A. Jupiter-masscompanion to a solar-type star, Nature 1995,378, 355–359.

Miller, S. L. The production of amino acidsunder possible primitive Earth conditions,Science 1953, 117, 528–529.

Munoz Caro, G.M., Meierhenrich, U. J.,Schutte, W. A., Barbier, B., Arcones Segovia,A., Rosenbauer, H., Thiemann, W.H.-P.,Brack, A., Greenberg, J. M. Amino acidsfrom ultraviolet irradiation of interstellar iceanalogues, Nature 2002, 416, 403–405.

Niemann, H.B et al. The abundances of con-stituents of Titan’s atmosphere from theGC-MS instrument on the Huygens probe,Nature 2005, 438, 779–784.

Ogata, Y., Imai, E.-I., Honda, H., Hatori, K.,Matsuno, K. Hydrothermal circulation ofseawater through hot vents and contributionof interface chemistry to prebiotic synthesis,Origins Life Evol. Biosphere 2000, 30, 527–537.

Ourisson, G., Nakatani, Y. The terpenoidtheory of the origin of cellular life: the evo-lution of terpenoids to cholesterol, Chem.Biol. 1994, 1, 11–23.

Paecht-Horowitz, M., Berger, J., Katchalsky, A.Prebiotic synthesis of polypeptides by het-erogeneous polycondensation of amino-acidadenylates, Nature 1970, 228, 636–639.

Pizzarello, S., Cronin, J,R. Non-racemic ami-no-acids in the Murray and Murchison me-teorites, Geochim. Cosmochim. Acta 2000,64(2), 329–338.

Schmidt, J. G., Nielsen, P. E., Orgel, L. E.Information transfer from peptide nucleicacids to RNA by template-directed synthe-ses, Nucleic Acids Res. 1997, 25, 4797–4802.

Schçning, K.-U., Scholz, P., Guntha, S., Wu,X., Krishnamurthy, R., Eschenmoser, A.Chemical etiology of nucleic acid structure:the Æ-threofuranosyl-(3’2’) oligonucleotidesystem, Science 2000, 290, 1347–1351.

Schopf, J. W. Microfossils of the Early ArcheanApex Chert: new evidence of the antiquity oflife, Science 1993, 260, 640–646.

Severin, K. S., Leem, D.H., Martinez, J. A.,Ghadiri, M. R. Peptide self-replication viatemplate-directed ligation, Chem. Eur.J.1997, 3, 1017–1024.

Terfort, A., von Kiedrowski, G. Self-replicationby condensation of 3-aminobenzamidinesand 2-formyl-phenoxyacetic acids, Angew.Chem. Int. Ed. Engl. 1992, 31, 654–656.

W�chtersh�user, G. Life in a ligand sphere,Proc. Natl. Acad. Sci. USA 1994, 91, 4283–4287.

Westall, F. Life on the early Earth: a sedimen-tary view, Science 2005, 308,366–337.

Wintner, E. A., Conn, M.M., Rebek, J. Studiesin molecular replication, Acc. Chem. Res.1994, 27, 198–203.


1.7.3Web Sites

Jet Propulsion Laboratory / NASA: Mars Mete-orites, 2003 http://www.jpl.nasa.gov/snc/

Schneider, J. 2003. http://www.obspm.fr/encycl/f-encycl.html.

2From the Big Bang to the Molecules of LifeHarry J. Lehto

This chapter deals with the evolution of the Universe that predatesboth chemical evolution and the evolution of life. First, the originof the elements critical for life is reviewed. The origin of hydrogenand helium is explained from cosmological models. Hydrogen isrequired when water is formed. Helium, which appears quiteuseless for life, turns out to be critical in the stellar synthesis ofcarbon leading to heavier elements. The second constituent ofwater, oxygen, is also formed in the hot cores of stars. Once theseelements are expelled from stars back into the cool interstellarspace, they get mixed into the interstellar clouds resulting in a vastspectrum of molecules. The observed properties of these moleculesand of the larger dust particles are reviewed. They play an impor-tant role in the formation of planets in the accretion disks of metal-rich populations of stars. This material, which is reprocessed by thenewly formed stars and other planets in the planetary system,“rains” on the young planet in the form of meteorites, comets, andasteroids, creating a supply of raw materials for the prebioticevolution and the eventual biological evolution of life. Theseprocesses are considered in the light of the formation of the Earth.

2.1Building Blocks of Life

Life as we know it is made of compartments, the cells. Within all cells similarmolecules are found, no matter which cell is considered.

• Water (H2O) is the basis for the cytoplasm of all cells: all theessential biological reactions take place in water. Water is alsoessential for transport of nutrients and waste. The elementsin water are quite obviously hydrogen (H) and oxygen (O) (seeChapter 1).

• Nucleic acids (DNA and RNA) are essential to present lifeforms in providing instructions on how to build proteins and

2.1 Building Blocks of Life 23


in transferring this information from one generation of cellsto the next. Nucleic acids are long polymers that consist ofnucleotide bases – cytosine, guanine, thymine, and adeninein DNA and cytosine, guanine, uracil, and adenine in RNA –joined by a backbone formed by a sugar – deoxyribose in DNAor ribose in RNA containing five carbon atoms – and aphosphate group, connecting the adjacent sugars. The ele-ments found in the nucleic acids are carbon (C), H, nitrogen(N), O, and phosphorus (P) (see Chapters 3 and 4).

• Amino acids are the building blocks of proteins. They are alsoquite complex molecules that are exclusively made of C, H, N,O, and sulfur (S) (see Chapter 3).

• Lipids are the fundamental molecules in cellular membranes.Normally, membranes are bi-layered with water-attracting(hydrophilic) layers on the outside and water-repelling (hy-drophobic) layers in the “internal” layers. The hydrophobiclayers are hydrocarbon chains, and the hydrophilic endsusually contain phosphate groups. The main elements inlipids are C and H, but O, N, and P are also used in thehydrophilic ends.

• Carbohydrates, comprising sugars, starches, collagens, orcellulose, are important for all life forms. Carbohydrates areenergy-rich compounds that function as energy-storage andstructural compounds in cells. On the first level, they areproduced by autotrophic life forms by reducing CO2, either byusing energy derived from geochemical compounds or bybinding solar energy. The sugars deoxyribose and ribose playan essential role in forming the backbone of the DNA andRNA. The essential elements in carbohydrates are C,H, andO.

During the dawn of life the prebiotic formation of these complex molecules tookplace through simpler precursor molecules. These are most likely H2O, form-aldehyde (H2CO), hydrogen cyanide (HCN), small sugars (CH2O)n, ammonia(NH3), methane (CH4), and other hydrocarbons –(CH2)n– (see Chapter 3).Six elements, namely C, H, O, N, S, and P, make up 98% of all living tissue. They

are the most important elements of known life. The remaining 2% of living tissueis made of other elements. The exact list of trace elements differs somewhat amongauthors. There is common agreement that the most important trace elements aresodium (Na), chlorine (Cl), potassium (K), fluorine (F), calcium (Ca), iodine (I),magnesium (Mg) and iron (Fe). Ca and F are needed for external skeletons; K, Na,Cl, and I for nervous systems; and Mg and Fe for chlorophyll and hemoglobin,respectively. K, Na, and Cl are needed for maintaining the correct osmotic pressureof cells.Some authors suggest a list of less important trace elements, such as boron (B),

aluminum (Al), silicon (Si), chromium (Cr), manganese (Mn), copper (Cu), zinc

2 From the Big Bang to the Molecules of Life24

(Zn), selenium (Se), strontium (Sr), molybdenum (Mo), silver (Ag), tin (Sn), lead(Pb), nickel (Ni), bromine (Br), and vanadium (V). Other authors would removesome elements or add some other ones. The need for specific trace elementsdepends on the species and its environment.In summary, one may conclude that approximately 25–30 elements are needed

for life. The remaining 80 elements are not essential and often turn out to bedetrimental to life.

2.2Big Bang: Formation of H and He

At the beginning, the Universe was small, dense, and hot and there were noelements. What happened during the first 10–43 seconds is beyond the realm ofphysics. At 10–43 seconds the temperature was 1019 GeV (for convenience, 1 eV k–1

~11 605 K, so 1 GeV corresponds to 1013 K; k is the Boltzmann constant). Hence,1019 GeV corresponds to a temperature of 1032 K, a number so high that it is hard toimagine.When considering the evolution of the early Universe, the single most important

parameter is temperature. The physics of the early Universe is easiest to under-stand in terms of temperature because equations of state of its different compo-nents are most conveniently calculated as a function of temperature. The begin-ning of the Universe took place some 13.7 € 0.15 billion years ago. The Universestarted to expand immediately (Fig. 2.1).The Universe was dominated by radiation. Elementary particles changed con-

tinuously to radiation and vice versa. At 10 GeV, when 0.01 �s had elapsed,particles called bosons started to decouple from radiation; protons, neutrons,and mesons began to form. This continued until temperature fell to about100 MeV (1012 K), when the temperature of the Universe became too low for theformation of these particles. At this point all protons, neutrons, and mesons wereformed. In the meantime, about 100 �s had elapsed. Later, the protons wouldbecome the nuclei of hydrogen atoms, and neutrons and protons would combine toform alpha particles or helium nuclei. The Universe continued expanding and itstemperature fell.Within the next second the temperature fell enough for the formation of

electron-positron pairs. Most of these pairs annihilated back to radiation, butbecause of an antimatter-matter symmetry, a surplus of electrons was left.For astrobiology, the next relevant moment in the evolution of the Universe was

the time of nucleosynthesis. It started at about 1 s from the beginning, when thenumber of photons in the Universe, with energies smaller than 2.2 MeV, corre-sponding to the binding energy of a deuteron (proton + neutron) fell below thenumber of neutrons. The nucleosynthesis continued for about 5 min, until thetemperature fell to about 70 keV (or 8 � 108 K). The number of neutrons duringthis era was such that there was 1 neutron (nn) for 7 protons (np). This fixed themass ratio of helium (He) to hydrogen (H) at:

2.2 Big Bang: Formation of H and He 25

2 nnnp

� �

1þ nnnp

� � ¼ 14

(2.1).

At that time, almost all neutrons became bound to He. In addition, some lightnuclei lithium (Li), B, and beryllium (Be), as well as 3He and deuterium (D), wereformed around this time. Heavier nuclei did not form because there are no stablefive-nucleon nuclei and because heavier nuclei would have required the presence ofHe nuclei and even higher temperatures. Within the next few minutes, the Henuclei were formed, and the last remaining neutrons decayed with a half lifetime of615 s (or a mean lifetime of 886 s).When the temperature of the Universe fell to T = 0.8eV or 9284 K (t = 47 000

years) it was time for photons to decouple from matter. The Universe became


Fig. 2.1 Evolution of the early Universe (Image credit: ESA).

matter dominated. Relatively soon, at T = 0.3 eV or 3 000 K, or 380 000 years fromthe Big Bang, the average background photon encountered its last scattering.The distant faint glow of the temperature (and matter) fluctuations of that

moment can be seen as the cosmic microwave background. Around the time ofthe last scattering, the temperature had fallen enough so that atoms could alsoform. Protons combined with electrons into H, and two electrons and an alphaparticle formed He atoms. The scale factor (a sort of a measure of size) of theUniverse at the time was about 0.09% of the present value.The production of light elements in the Big Bang was first calculated in 1948 by

Ralph Alpher, Hans Bethe and George Gamow. They predicted a microwavebackground radiation of 5 K. This basic idea was then confirmed in 1964 by theNobel-winning, serendipitous observations of background radiation by Penziasand Wilson. They measured the temperature to be 3 K. More recently, in 1990, theobservations from the NASA satellite Cosmic Background Explorer (COBE) showedthat the radiation spectrum of the cosmic microwave background follows veryaccurately a blackbody spectrum.In 2003, the Wilkinson Microwave Anisotropy Probe (WMAP) team led by Charles

Bennett from John Hopkins University provided the best fit to the temperature ofthe microwave background, with a temperature of T = 2.725 € 0.002 K. Theseobservations were further analyzed by subtracting from each point the averagespectrum of the sky and by removing the dipole component, which is at a level ofabout 3 mK and is caused by our movement with respect to the microwave back-ground. In addition, the galactic contribution to the background was removed –this is radiation found mostly on the galactic plane. One was left with temperaturefluctuations frozen to the background at the time of the last scattering. They showup as tiny ˜T ~10–5 K fluctuations in the background. By measuring the correla-tions in these fluctuations over different angular scales over the whole sky down toabout 0.3 degree, one can calculate a two-point correlation function. This can thenbe compared to various cosmological models.The model that best explains the observed distribution is a Universe that

experienced a rapid expansion or inflation starting at 10–35 s from the beginningand lasting for 10–32 s. Furthermore, the present conditions of the Universe aresuch that it is expanding at a rate of a Hubble constant, which has ameasured valueof H = 71 € 2 km s–1 Mpc–1 (pc = parsec, a unit of astronomical length, with1 pc » 3 � 1016 m). The average density of the Universe is equal to the criticaldensity within a measurement error of 2%. The critical density is the averagedensity of the Universe at which the geometry of the Universe is flat:

æ ¼ 3H2=8�G � 1:0� 10�26g cm–3, (2.2),

where H = Hubble constant and G = gravitational constant.The observed statistical properties of the microwave background have been

explained by invoking the presence of dark energy. Mathematically, this corre-sponds to the cosmological constant, which was introduced to the standard Fried-man equations by Albert Einstein. He did not like the idea that the Universe could

2.2 Big Bang: Formation of H and He 27

be non-static and added ad hoc his cosmological constant. For decades, thisconstant was considered a curiosity, but now, with the latest microwave data, ithas become quite useful again.About 73% of the energy density in the Universe is in the form of dark energy. At

present it is not knownwhat this is physically or theoretically, but it can bemathemati-cally understood as the energy density of vacuum. Its presence is also suggested by theaccelerating expansion rate detected from observations of supernovae and some otherobservations. The remaining 27% of the energy density is matter. About 85% of thismatter is “dark matter.” The physical nature of this matter is not yet known, but itsinfluence can be seen, e.g., in orbits of stars in galaxies or in the velocity dispersion ofgalaxies in galaxy clusters. The remaining matter (15% of matter and 4% of the totalenergy density) is baryonicmatter,mainlyH andHe.Heavier elements constitute 1%of the combined H and He mass only. Thus, assuming that the dark energy is real,only about 0.04%of the density of theUniverse is in the formof heavier elements suchas C, N, O, or Fe, which are the elements life is made of (Fig. 2.2).

2.3First Stars: Formation of Small Amounts of C, O, N, S and P andOther Heavy Elements

After the last scattering of the photons, a dark era followed in the Universe(Fig. 2.1). No stars existed for another 100–300 million years. It took about thattime for the first gas clouds to collapse and form the first stars. The details of thephysics of those stars and the exact timescales of their formation and evolution arestill unclear. Using the Spitzer Space Telescope, faint infrared (IR) fluctuations in thecosmic IR background were measured by Kashlinsky and his collaborators in late2005. They argue that the fluctuations are caused by combined light from a largenumber of the very first stars. No individual stars are seen. The ultraviolet (UV)


Fig. 2.2 Components of the Universe. Darkenergy: 73%; cold dark matter: 23%; baryonicmatter, which is mostly H and He: 4%; neutri-nos: 0.3% (dark gray sector); heavier elementssuch as O, C, and N: 0.04% (white sector). Thelast sector is the sector of life.

emission from the stars is now observed as highly red-shifted radiation in the IR.This radiation could well come from the very first stars.It is likely that these are the only stars that formed along the lines first described

by Jeans in 1902. A gas cloud, which was at that time made of H and He, started tocollapse under its own weight. The collapse is initiated if the mass of the cloud islarger than the Jeans’ mass:

Mcloud> MJM = 700 M� (T / 200 K)1.5 (n / 106)–0.5 (2.3),

where n = the number density of particles (H andHe) per cm3, T = the temperatureof the cloud in K, andM� = the solar mass, a basic mass unit in many astronomicalcalculations.Thus, if the cloud has a density of n = 106 cm–3 and a temperature of T = 200 K,

then a cloud exceeding a mass of 700 M� would be able to collapse. If the temper-ature is higher than T = 200 K, then the cloud should be more massive for the totalgravitational attraction to overcome the added pressure caused by the increasedtemperature. Similarly, if the gas density is higher than n = 106 cm–3, then asmaller cloud could collapse according to this model.As the collapsing proceeds, the density in the cloud center increases. With the

increased density the pressure at the center increases, as does the temperature.Finally, in the central 1% or so, the temperature of the cloud rises to 4 � 106 K, andnuclear reactions begin. There appears to be no clear reason for an upper limit ofthe mass of a star formed in this way. It is possible that the very first stars hadmasses of 100–300 M�, or even as large as 500 M�. These very massive stars livedshort lives of only one million years or so and produced the first heavier elements,such as C, N, O, P, S, Al, and Fe. At the end of their lives, they exploded and shed allthese new heavy elements into the surrounding, still quite dark space. These earlystars are now referred to as population III stars. The first galaxies formed when theUniverse had an age of maybe 600–800 million years. All the stars formed in thesenew nascent galaxies have a minutely tiny seed of heavier elements in addition tothe overwhelmingly abundant H and He.

2.4Normal Modern Stars, Bulk Formation of C, O, N, S, P and Other Heavy Elements

Stars can be classified by several different means. The most important classifica-tion scheme is the Hertzsprung-Russell (HR) diagram (Fig. 2.3). A version of theHR diagram, the color magnitude diagram, shows the brightness of the star, e.g., Vmagnitude, as a function of its color, e.g., brightness difference in two bands, saythe blue and visual (B – V). Several variations of this diagram exist. If the distanceto a star is known and its apparent brightness is measured, then its luminosity canbe calculated. If a spectrum of the very same star also can be obtained, then thetemperature of its photosphere can be determined. By doing this to a multitude ofstars, an HR diagram in a form that is more relevant to astrobiology can be drawn.

2.4 Normal Modern Stars, Bulk Formation of C, O, N, S, P and Other Heavy Elements 29

Here, the brightness of the star, given as logarithm of luminosity, is plotted againstthe logarithm of temperature.If the star is assumed to behave like a perfect blackbody radiator, which is a

reasonable assumption in this context, then straight lines of constant stellar radiican be drawn into this plot. Furthermore, if the luminosity and the temperature ofthe central star are known, the distance of the habitable zone can be included inthis same plot. This is shown in Fig. 2.4 on the right. This assumes the definition ofa habitable zone, put forward by Kasting, as the region around the star where thetemperature is such that water stays liquid (see Chapter 6). The lower edge of thistemperature range is close to 0ºC at a range of pressures, but the higher enddepends on the atmospheric pressure of the planet itself. At 105 Pa (1 atm) it is100 �C, but at 2 � 105 Pa it is 121 �C.Because habitability depends on the luminosity of the central star, the distance of

the habitable zone is set on approximately horizontal lines on the diagram. Consid-


Fig. 2.3 Schematic representation of a Hertz-sprung-Russell (HR) diagram; it shows the startemperature or spectral type as abscissa andstar luminosity or absolute magnitude asordinate. Temperature of stars decreases from

left to right with the spectral type sequence ofstars: O, B, A, F, G, K, M, to L. The diagonallines at 100, 1, and 0.01 represent theapproximate radius of the star in solar radii.

ering the limitations, several areas of the HR diagram can be ruled out as ratherunsuitable for life. Even the most optimistic views of habitability can be condensedinto a triangle (Fig. 2.4). Thismay be an area where life could, in principle, form. Forlife to evolve to a higher evolutionary stage, the conditions on the central star shouldstay relatively stable for at least one billion years. This would narrow the starssuitable for life as we know it down to a narrow ellipse-like zone (Fig. 2.4).There is one additional stellar property that is relevant to astrobiology not shown

in the HR diagram. It is what astronomers call metallicity (Z), which is the massfraction of elements heavier than hydrogen and helium. Solar metallicity abun-dance is about 1–2%. Hot, bright stars tend to have high metallicity and faint redstars usually have low metallicity. However, this may not represent a propercorrelation but rather a manifestation of the age of the average star of these spectralclasses. Blue, bright stars are short-lived, but faint red stars are of very differentages, including some that are almost as old as the Universe.The young stars are called population I stars, and the old ones are called

population II stars. Our Sun is a population I star. The different populations ofstars have different roles in astrobiology.


Fig. 2.4 Biological HR diagram; lines of a typicaldistance of the habitable zone (HZ) are shown onthe right of the diagram (scaling that of the Sun atHZ = 1.0). Because the range of the HZ dependson the luminosity of the central star, the distances

areset on approximately horizontal lines on thediagram. The triangle (dashed line) describesthe range where life in principle could form. Thenarrow ellipse-like zone describes an area wherelife might evolve to a higher evolutionary stage.

The first normal stars were formed from very metal-poor gas. There were somemetals around from the very first stars, but the amounts were very low. Even withsuch low concentrations of metals, such as C, the nuclear reactions in stars got animportant boost because these metals are used as catalysts, e.g., in the carbon–nitrogen–oxygen (CNO) cycle. These first normal stars were also the primaryfactories for the heavier elements, which are important for life.The evolution of a single star is determined mainly by its mass. (Binary stars exist

quite commonly, but the theory of binary star evolution will not be considered here.)If the mass of a single object emerging from a collapsing cloud is smaller than about0.08 M�, then its core will not have a high enough temperature to start the fusion ofH into He. If the stellar mass is larger than 0.08 M�, and less than 0.26 M�, thecentral temperature will rise above 4 � 106 K and He production will start at a veryslow pace in the center of the star by the proton–proton chain reaction (p–p chainreaction). Two protons combine to form a deuteron, which then combines with afurther proton to form 3He. Finally, two 3He combine to form a 4He and two protons.The final step can also proceed through a loop involving Li, B, and Be, essentially withthe same end result. This process will continue throughout the lifetime of the star.Stellar models suggest that these stars will stay convective and well mixed. The

same models indicate that their lifetime is in the range of 1011–1013 years. This ismuch longer than the present age of the Universe. None of them have beenwitnessed to “die.” It is thought that after a very long time these stars will endup as white dwarfs. The energy within these stars is transferred via convectionfrom the center of the star through buoyant, hot material rising from the centralparts of the star and cooler material near the surface sinking down.In stars of masses larger than 0.26 M�, elements heavier than He will also form.

Pressure and temperature increase towards the center of a star. It is in the verycenter of the star where most of the nucleosynthesis takes place. The evolution ofstars heavier than about 0.26 M� can be divided into two broad groups with thedividing line at about 1.5 M�.The evolution of a solar type star of mass 0.26 M� < M < 1.5 M� is approximately

as follows. These stars form initially with a central temperature higher than4 � 106 K. The central parts become radiative, while the outer parts stay convective.The p–p chain reaction is the main source of the stellar luminosity for these starsduring the main sequence phase of the star, which lasts about 2–20 billion years.During this time the star is relatively stable. Close to the end of the main sequencephase, the star has developed a helium core that is degenerate, meaning that it isnearly incompressible. Around this core there is a hydrogen fusion envelope thatstarts to expand. The star becomes a red giant.The temperature of the He core increases, until suddenly, when the temperature

reaches about 108 K, the so-called triple-alpha reaction sets in. In this reaction He istransformed into C. Two He nuclei combine into a 8Be nucleus, which is unstable.If a third He nucleus interacts within 3 � 10–16 s, then a 12C nucleus with anemission of a photon results; otherwise, the 8Be decays back to two He nuclei.This reaction requires the near-simultaneous collision of the three He nuclei(alpha particles) and is therefore called the triple-alpha reaction.


The onset of the triple-alpha reaction across the core is so sudden (few hundredsof seconds) that it causes a He flash, the inner parts of the star collapse, and theouter parts of the star take the extra energy. Later, around the central parts, triple-alpha reactions continue in a He shell. This He shell is surrounded by a H shell,where He is produced by the p–p reaction. The outer envelope expands further, andeventually the star loses the outer shells as an intense stellar wind. A planetarynebula with a hot star in the center results. (It should be emphasized that physicallythe planetary nebula has nothing to do with planets or planetary systems. Thename “planetary nebula” reflects the appearance of these objects as seen byrelatively small telescopes. They tend to look round, not point-like as stars do,and thus are reminiscent of the appearance of planets such as Jupiter or Saturn.)The central star in planetary nebulae is often not visible by small telescopes, butlarge telescopes reveal that the end of the life of a solar mass it to become a whitedwarf. The white dwarf is made mostly of He, but it has a C or O core, and on thesurface it may have a thin outer layer made of H.The gas in the stellar wind during the red giant phase and the planetary nebula

phases consists mainly of H and He, but it also contains about 2% C, N, and O,which are released into the interstellar medium (ISM). Elements heavier than Oare not produced in these stars. Because these lighter stars are substantially morecommon than more massive stars, they have been suggested to be a significantsource of new C, N, and O in the present galaxy.Stars more massive than 1.5 M� have such a high central temperature

(> 18 � 106 K) that a different nuclear fusion mechanism takes over in the con-version of H to He. At these high temperatures the CNO cycle becomes moreeffective than the p–p cycle. One should note that in a CNO cycle, also known as thecarbon cycle, no C is produced; instead, C is needed as a catalyst. The carbon cycleproceeds as follows:

12C + 1H �13N + ª (2.2 a)

13N�13C + e+ + �e (2.2 b)

13C + 1H �14N + ª (2.2 c)

14N + 1H�15O + ª (2.2 d)

15O�15N + e+ + �e (2.2 e)

15N + 1H�12C + 4He (2.2 f)

Reaction (2.2 d) is the slowest one and it determines the total reaction rate. It isimportant to note that this bottleneck creates a surplus of N. Although C is acatalyst in this reaction, it effectively transforms some C into N. Even if the carboncycle is the main source of N in the Universe, the main benefit of this reaction isthe efficient conversion of H into He.


In these stars the very center of the star will be convective and the outer parts willremain radiative. As in the less massive stars, a He core will eventually form andthe star will become a red giant. Now, however, the He core remains convective,and the onset of He fusion into C by triple-alpha reaction starts at a more leisurelypace; no He flash takes place. A shell-like structure forms, with C in the centersurrounded by He and H shells. Stars in the mass range of 1.5 M� < M < 3 M� willpass through a red giant phase and end up as white dwarfs.The evolution of stars in the range of 3 M� < M < 11 M� is not well understood

theoretically. It appears that in the range of about 3 M� < M < 8 M� the C core willnot ignite and the star will evolve through a red giant phase and end up as a whitedwarf, with the outer parts of the star expelled in a strong stellar wind.In more massive stars (M > 8 M�), the C core will ignite, and a C flash will take

place. Here, the main reaction combines two C, creating an O nucleus and two Henuclei. Later, if the degenerate center has a high enough temperature, two O nucleicombine either into a Mg nucleus and two He nuclei or into one Si and one He. Inthe heaviest stars two Si nuclei combine into one Fe nucleus. All other elementsfrom C to Fe are formed as well. The nuclear reactions producing these elementsare more complex. The conditions at the center of the star will eventually determinewhich are the heaviest nuclei formed. Depending on the mass of the star, an onion-like structure will eventually form with an O, Si, or Fe core. All heavy elements upto Fe and Ni can be formed in these stars as products or side products of the above-mentioned reactions.If the mass of the star is about 8 M� < M < 11 M�, the star will end up with an

O/Ne/Mg core. Thiswill eventually turn into anO/Ne/Mgwhite dwarf, with the outerparts of the star blown out in a fierce stellar wind. Other models suggest that the fateof these stars is to end up as a supernova with a neutron star remnant. In either case,the lighter elements in the outer shells will be expelled into the interstellar space.Stars heavier than about 11 M� have been studied theoretically more extensively.

They will end up with a shell-like structure with Fe in the center, which impliesthat all nuclear fuel in the core has been exhausted. The core will collapse on adynamical timescale, which is on the order of a few hours. The rebounce from thiscollapse will create a shock traveling outwards, resulting in a supernova explosion.The whole mass of the star and all the elements it contains are thrown into thesurrounding space. It is also possible that the center part of the star, the Fe core,will collapse into a black hole or a neutron star, but the outer parts of the star willstill be ejected into space. Supernova explosions have been the main means forliberating the heavier elements into the interstellar space.Elements heavier than Fe are formed in stars in small amounts by the slow

neutron-capture (s) process and in supernovae by the rapid neutron-capture (r)process. These two mechanisms have somewhat different isotope distributions.The heaviest elements formed in the s-process are 208Pb and 209Bi. In the r-processthe heaviest elements are thought to have an atomicmass of about 270. The formationof some rare isotopes such as 190Pt cannot be explained by the s- or r-processes.These are thought to have formed in a supernova explosion by the proton-capture (p)process. Table 2.1 shows a few properties of some main sequence stars.


Table 2.1 Properties of main sequence stars.

Spectral class Mass (M�) Temperature (K) Age (109 years)

O5 30 44 000 0.005A0 3 12 000 0.24F2 1.5 7 200 2G2 1 5 700 10M0 0.5 3 800 30M7 0.1 2 800 10 000

2.5The First Molecules (CO and H2O)

The most common molecule in the interstellar space is molecular hydrogen (H2).The next most common molecules are carbon monoxide (CO) and water (H2O).These are very interesting molecules because they already contain the heavierelements important for life. The elements making up these molecules were formedin stars that have already ended their life. Walter and coworkers have observed withthe Very Large Array (VLA) situated in New Mexico, USA, the presence of CO inthe spectrum of the quasar SDSS J1148+5251, which has a redshift of z = 6.419.Based on present models of the Universe, this means that these molecules werealready formed 800 millions years after the start of the Universe; thus, at this timethe first ingredients for life were available. The presence of CO indicates thatsubstantial amounts of both C and O had already formed. H2O has not beendetected from this quasar, because of observational limitations, but one can inferits presence because it is formed in a way similar to CO, directly from gaseous Hand O.

2.6Interstellar Matter

Aboriginal Australians see a long, dark emu bird in the sky, with the bonfires oftheir forefathers lighting up the stars of the sky (Fig. 2.5). The “emu” is formed by amultitude of individual dark clouds in the plane of our galaxy. The presence ofinterstellar matter manifests itself also as bright illuminated patches in the skyviewable even with ordinary binoculars. Some of the best examples are Orionnebula M42 and several clouds in Sagittarius and adjacent constellations.The space between stars was thought to be void until Trumpler (1930) noted that

the calculated linear size of open clusters seemed to increase with the distance.Clearly, because such a correlation should not exist, one could reason that distancesto more distant clusters were overestimated. This could only be caused by some

2.6 Interstellar Matter 35

interstellar dust particles scattering part of the light away on its way from thecluster to our telescopes. At present, it is known that this extinction is on averageabout 2 mmag pc–1 (or 0.06% per light year).The presence of interstellar matter is deduced in several ways. In the optical

region, extinction is one of the most important proofs of interstellar matter. Asecond indication of matter in interstellar space comes from studying two stars thathave similar spectral properties, which means that they have similar intrinsicbrightness and temperature. If one then compares the observed spectrum of themore distant star with that of the closer star, then one can note that it is reddened,which means that light in the blue end of the spectrum is scattered away comparedto the red end of the spectrum. It is a phenomenon similar to that of the reddeningof the Sun as it gets close to the horizon, in which case the scattering is caused bythe tiny O2 and N2 molecules of the atmosphere (Rayleigh scattering). In inter-stellar reddening, the scattering is caused by dust particles in the interstellar space,which are on the order of the wavelength (Mie scattering) in size.The third manifestation of interstellar matter can be observed by studying the

polarization of the starlight. Interstellar dust particles align themselves preferablyalong the feeble galactic magnetic field. As light from a star travels towards us,some light is scattered. Because of the shape of the particles, this scattering has apreferred direction: perpendicular to the longer axis of the particle, meaning thatlight passing through a population of dust particles will have a preferred directionof oscillation, i.e., it will be linearly polarized. By studying this polarization, onemay infer the presence of interstellar non-spherical dust particles and even meas-ure the direction of the galactic magnetic field in different parts of the sky. Bycombining the polarization with the reddening, one obtains the first estimate of thesize and shape of interstellar dust particles.


Fig. 2.5 “Emu.” (a) Constellation showing the emu bird in thesky (Photo credit: H. Lehto. La Silla, Chile, 5 March 2006).(b) A real emu bird (Photo credit: H. Lehto, Northern Territory,Australia, 8 August 2003).

The fourth signature of the presence of intervening interstellar matter are theinterstellar absorption lines in the spectra of stars. Most of the absorption lines instellar spectra are formed in the stellar photosphere, but by studying the Dopplershift and the shape of the individual absorption lines, astronomers can identifyinterstellar lines from the intervening matter and deduce the properties of theinterstellar gas. Note that of the four methods described above, extinction, redden-ing, and polarization measure the properties of the particles, while only one, thespectral absorption lines, indicates the presence of interstellar gas, although themass of the gas outweighs the dust by about 100 to 1.The most common gas in the Universe, H, emits radiation at a wavelength of

21 cm. This radio photon is caused by a small change in the H when the singleelectron orbiting the proton changes its spin direction from being of the oppositesense to being in the same sense as the proton’s spin. Technically speaking, thespin axis changes from antiparallel to parallel. It is very unlikely to happen to asingle atom, as it happens about once in 10 million years, but because there is somuchH along any line of sight, all the added changes shine quite brightly at 21 cm,particularly in the plane of the galaxy. Because practically nothing absorbs thiswavelength, it has proven to be one of the most useful tools in mapping thedistribution of interstellar H in our galaxy. It were these measurements thatshowed that gaseous neutral H (HI) is distributed along spiral arms. Because His the main constituent in the interstellar gas, this study also shows where the bulkof interstellar gas resides. Note that HI refers to neutral H, HII to (singly) ionizedH, and H2 to the molecular H2. All these are important constituents in differentparts of the interstellar medium (ISM).Several different phases of interstellar gas are known, with the coldest and

densest gas being found in molecular gas clouds and the most tenuous and hottestgas, e.g., in supernova remnants. The cold, dense clouds are considered in moredetail in the next section.With the advent of space observatories, extensive IR observations became pos-

sible. These have opened a completely new window for the study of interstellarmatter in its many forms. These observations are discussed in the context of coolinterstellar clouds (Section 2.6.1) and interstellar ice and dust (Section 2.6.3).

2.6.1Interstellar Clouds

The distribution of interstellar dust is not uniform. It is concentrated into inter-stellar clouds that are typically located on the inner edges of the galactic spiralarms. Visually, these clouds appear as dark areas in the sky with much fewer stars;in fact, some of them are optically so opaque that they appear as totally starlesspatches of the sky (Fig. 2.6). Optically, the clouds have such a high extinction thatpractically the only means for studying them is in radio and infrared wavelengths.Spectroscopy in radio wavelengths has two functions. One function is the search

for different molecules. This is done at a large range of wavelengths. From anastrobiological point of view, the most interesting ones are to be found in the


millimeter ranges. The second function, the spectroscopy of CO, OH, SO, SO2,andother molecules at centimeter and decimeter wavelengths, is critical because itprovides the means for measuring the matter distribution, temperature profiles,and internal motions within the clouds. All this has important implications forunderstanding under which physical conditions complex molecules, dust particles,and ices are formed.IR spectroscopy is the means for studying the properties of dust grains by

looking at signatures of various ices and minerals in the IR emission spectra ofinterstellar clouds. As the extinction in IR is not as severe as in the optical, one canactually recognize at these wavelengths also newborn stars and their accretion


Fig. 2.6 Pre-collapse black cloudBARNARD 68. Picture taken by theFocal Reducer/Low Dispersion Spec-trograph (FORS) team on 10 January2001 with the ANTU telescope unit ofthe Very Large Telescope (VLT) locatedon Cerro Paranal in the Atacama Desert,northern Chile (Image credit: EuropeanSouthern Observatory [ESO]).

Fig. 2.7 (a) Orion nebula M42, in the opticalrange. The bright cloud is illuminated by thestars of the Trapezium cluster, which have anage of about 2 million years. (b) Behind theveils of these clouds, a dense molecular cloud

resides, within which hundreds of newlyforming stars are seen in IR. (A: Photo credit:H. Lehto, Tuorla Observatory, Finland, 24January 2004; B: Image credit: ESO).

disks still surrounded by the blown-away dust shrouds in the depths of the gascloud.The densest of the clouds, the giant molecular clouds (GMC), are completely

opaque at visual wavelengths. The presence of large amounts of H2 is theircharacteristic signature, but they contain also atomic H, inert He, and about 1%of heavier elements. The temperature in the densest parts is 10–20 K. The den-sities, measured in “particles” of mainly H atoms, H2 molecules, and He, can be ashigh as 109 particles per m3, and up to 1012 particles per m3, depending on thecloud. A density of 1012 particles per m3 corresponds to about 10–11 g m–3 or, lessconventionally, 10 mg km–3. For comparison with more familiar units, the densityof the Earth’s air is about 1300 tons km–3. Still, from an astronomical point of view,these clouds are very dense.As an example, one may consider the closest GMC, the Orion cloud. It is at a

distance of about 500 pc and is about 120 pc in extent. From radio and IRobservations, it is known to have an apparent diameter of about 20 degrees inthe sky, or 40 times larger than the moon. One can see the outer edges of the Orioncloud also usually, as the young stars in the Trapezium illuminate the edge of theclouds and create a bright patch known as Orion nebula M42 (Fig. 2.7.A). Thedensest part of the cloud associated with M42 has a diameter of about 25 pc.Examples of the darkness of these clouds can be seen elsewhere in the dense partsof the Orion cloud, e.g., in the dark Horsehead nebula (Fig. 2.8).

2.6.2Interstellar Grains

2.6.2.1 FormationInterstellar grains play a critical role in the formation of interstellar molecules.Interstellar grains are formed mainly in the outer shells of stars when they are intheir red giant or asymptotic giant branch (AGB) phases (M giants, carbon stars, orradio luminous OH/IR stars). Some dust is formed in supernova remnants, novae,


Fig. 2.8 The dark Horsehead nebulain the Orion cloud, observed by theVLT Kueyen and FORS2 (Credit: ESO).

planetary nebulae, and WC stars and in circumstellar shells around supergiants.The presence of the grains is seen in the opacity caused by the dust and in thermalcontinuum IR emission from the dust. The details of the initial phase of the dustformation, the nucleation, are not well understood. Recent observations suggestthat crystallization of SiO2 takes place directly from the gaseous phase when thetemperature in the stellar wind falls below 700 K. The dust particles grow further inthe tenuous atmospheres of giants and, because of radiation pressure, are drivenaway from the star. The terminal velocity depends on the size of the grain and thematerial – or the mass of the grain. The fastest dispersing grains have a size ofabout 50 �m. Once formed and ejected into the ISM, the dust particles undergovarious kinds of reprocessing, causing both breaking up and growing. The extinc-tion curves observed optically require that a large fraction (>40%) of interstellargrains be >100 nm; therefore, some rebuilding or formation of grains must takeplace in the ISM, possibly in high-density regions by accretion to preexisting graincores.

2.6.2.2 Observed PropertiesIR spectra of ISM show signatures of a population of grains with small radii(a < 10 nm) that absorb about half of the energy emitted by the stars. This radiationis later reemitted in the IR. These grains are believed to be carbonaceous in nature.The smallest of them contain less than 100 C atoms and have tiny sizes (a < 1 nm).They create the IR emission bands characteristic of aromatic carbonaceous rings at3.3 �m, 6.2 �m, 7.7 �m, 8.6 �m, 11.3 �m, and 12.7 �m. The details of the bands arewell explained by a family of large molecules called polycyclic aromatic hydro-carbons (PAHs). Structurally, the molecules are two-dimensional sets of aromaticcarbon rings, consisting of 6 C atoms and each ring connected to each other. The Ccore is surrounded by an outer shell of H atoms. Structurally, the PAHs appearsimilar to pieces of chicken wire made of hexagons. However, precise ground-based laboratory spectra of these molecules are still missing for comparison.Furthermore, a spectral feature at 3.4 �m has been attributed to aliphatic hydro-carbons, which are chain-like in structure.The dust continuum emission in the 25-�m and 60-�m IR bands of the Infrared

Astronomy Satellite (IRAS) has been attributed to slightly larger carbonaceous verysmall grains (1 nm < a < 10 nm). The far-IR continuum radiation is furtherascribed to big grains (a ~ few 10 to few 100 nm), possibly a mixture of largegraphite and silicate grains.Dusty stellar envelopes show broad featureless bands at 10 �m and 20 �m in

both emission and absorption. They have been attributed to amorphous silicates.Recently, additional bands have been observed in the 10–45 �m region. They havebeen attributed to highly ordered crystalline silicates such as Mg-rich olivine(forsterite, Mg2SiO4) or pyroxene (enstatite, MgSiO3). These minerals have notbeen directly seen in spectra of ISM. As a curiosity, a 21-�m IR emission band insupernova remnants has been attributed to tiny diamonds. Their sizes are in therange 0.005–5 �m.


Depletion of gaseous C, Si, Mg, Fe, and O in ISM suggests that these elementsare used in another phase, possibly as silicates and metal oxides in grains. It shouldbe emphasized that graphite has not been unequivocally detected in the ISM,although it is quite often used as a model.Interstellar matter can be searched for locally in our Solar System. Using isotopic

traces, interstellar grains can be identified in pristine meteorites. They differsomewhat from the particles detected spectroscopically in the ISM. The mostcommon pre-solar grains that have been found are diamonds (2 nm in diameter),SiC (0.05–10 �m), graphite (0.4–6 �m), and Al2O3.High-velocity interstellar particles have been observed in the Solar System with

the detectors of the International Solar Polar mission Ulysses and from radarstudies of meteoroids. The sizes of these particles are about 0.8 �m and 15–30 �m, respectively. They are somewhat larger than typical interstellar grains.

2.6.3Ices

Spectral signatures of ices have been seen in OH/IR stars and other evolved stellarsystems, in lines of sight towards field stars located behind molecular clouds, andaround embedded protostellar objects. More than 20 ice features have beendetected in the IR. Ices create mantles on dust grains. These mantles are importantfor the formation of molecules.H2O ice was detected by Gillett and Forrest in 1973 from the 3-�mwaterline. It is

the most dominant solid-state species, and abundances of other ices are usuallygiven in reference to H2O ice. In clouds with substantial extinction, it is compa-rable in amount or even more abundant than gaseous CO. H2O ice is usually thesecond most abundant molecular species after H2 ([H2O]/[H2] ~ 10–4–10–5). About15–20% of the cosmic H2O is locked in ices, and the remainder is in gas phase.CO2 ice is difficult to detect with ground-based telescopes because of atmos-

pheric CO2. Its firm detection was not established until the late 1990 s with theInfrared Space Observatory (ISO) mission. At present it appears that CO2 is thesecond most abundant ice after H2O ice, with the CO2:H2O ratio being on averageabout 15–20% .CO has been detected in icy form. Although it may conform 3–20% of the ice

component in the grain mantles, it is much more abundant in the gaseous phasethan in the solid phase.CH4 has spectral signatures that are difficult to observe from the ground. The

abundance of CH4 ices is typically 1–2% of water ice. The ratio of gaseous to solidstate is usually below unity, suggesting that CH4 is formed directly by hydro-genation of carbon on the surface of the grain.Formaldehyde (H2CO), the simplest of the hydroxyl group of ices, was detected

from ISO observations towards five massive protostellar envelopes with the typicalabundance of 1–2% to water ice.Methanol (CH3OH) is one of the key elements in interstellar ices, amounting to

up to 10% of water ice content. The formation of methanol ice is still debated. It


could be caused by hydrogenation of CO or by energetic processes followed byselective desorption enhancement effects.Sulfur-containing ices have been searched for, and only OCS has been detected

so far, with a very low abundance of about 0.1% to water ice. H2S has an upperlimit of 1% for the abundance.N2 and NH3 ices have been searched for, but they have not been reliably detected.

The difficulty with N2 is that the possible signal is extremely weak; in the case ofNH3, the difficulty is separation from other spectral lines.O2 and N2 are IR-inactive molecules, and the upper limits for O2 ice are quite

high: <6% of water ice. No detection of O3 or CO3 has been made, suggesting thatO2 is indeed quite rare. It has not even been found in gaseous form, suggesting thatthe lack of O2 is real and is caused by its high reactivity.Other ices that have been found include OCN– and NH4

+ at a maximum level of afew percent. Tentative identifications include HCOO–, CH3CHO, HCONH2, and(NH2)2CO.

2.6.4Molecules in the Gas Phase

2.6.4.1 Observed PropertiesThe gas phase of interstellar clouds consists of H and He, with H2 being the mostabundant molecule in dense clouds. The second most abundant molecule is CO.O2 and N2 have not been found in the ISM. The upper limit for the abundance ofgaseous O2 towards the dense cores of molecular clouds, deduced from observa-tions of the Submillimeter Wave Astronomical Satellite (SWAS), is [O2]/[CO] < 10–7.Radio observations from the sub-millimeter to centimeter wavelengths have

recovered signatures of about 130 different molecules. One-quarter of these donot contain C, three-quarters do contain C, and out of these, two-thirds containboth C and H (Table 2.2). Astronomers would call about 100 molecules “organic,”whereas organic chemists would give this name to only about 65 moleculesdetected in interstellar space. For astrobiology, the most relevant molecules foundare water (H2O), formaldehyde (H2CO), hydrogen cyanide (HCN), sugars suchas glycoaldehyde (CH2OHCHO), and aliphatic hydrocarbon chains up toH(C�C)5CN.Finding longer molecules is in principle possible, but it becomes more difficult

with each added atom. One reason for this is that the more complex the moleculeis, the rarer it becomes. Another reason is that more complex molecules also havemuch more complex spectra, and their unequivocal identification becomes moredifficult. This has been the case in several claims of the detection of the simplestamino acid, glycine. Some of these have appeared quite convincing. The thirdproblem with complex molecules is that one needs a reference microwave labo-ratory spectrum for each molecule, and they are not trivial to measure. Manyspectral lines in the microwave region still remain unidentified.


Table 2.2 Interstellar molecules.

Numberof atoms

per moleculeMolecule

2 IF, AlCl, C2, CH, CH+, CN, CO, CO+, CP, CS, CSi, HCl, H2, KCl, NH, NO, NS,NaCl, OH, PN, SO, SO+, SiN, SiO, SiS, HF, SH, FeO(?)

3 C3, C2H, C2O, C2S, CH2, HCN, HCO, HCO+, HCS+, HOC+, H2O, H2S, HNC,HNO,MgCN,MgNC, N2H+, N2O, NaCN, OCS, SO2, c-SiC2, CO2, NH2, H3

+, AlNC4 c-C3H, l-C3H, C3N, C3O, C3S, C2H2, CH2D+(?), HCCN, HCNH+, HNCO, HNCS,

HOCO+, H2CO, H2CN, H2CS, H3O+, NH3, SiC3

5 C5, C4H, C4Si, l-C3H2, c-C3H2, CH2CN, CH4, HC3N, HC2NC, HCOOH, H2CHN,H2C2O, H2NCN, HNC3, SiH4, H2COH+

6 C5H, C5O, C2H4, CH3CN, CH3NC, CH3OH, CH3SH, HC3NH+, HC2CHO,HCONH2, l-H2C4, C5N

7 C6H, CH2CHCN, CH3C2H, HC5N, HCOCH3, NH2CH3, c-C2H4O, CH2CHOH8 CH3C3N, HCOOCH3, CH3COOH, C7H, H2C6, CH2OHCHO, CH2CHCHO9 CH3C4H, CH3CH2CN, (CH3)2O, CH3CH2OH, HC7N, C8H10 CH3C5N (?), (CH3)2CO, NH2CH2COOH(?), CH3CH2CHO11 HC9N13 HC11N

Source: From Al Wootten with permission.

2.6.4.2 Formation of H2

H2 is the most abundant molecule in the Universe, yet it is a difficult molecule toobserve. All the observations have to be made from space-based observatories. In1970, the Copernicus satellite observed H2 electronic lines in absorption against UVbright stars. The ISO operating at IR changed the level of knowledge. Rotationallyvibrated lines from 2–18 �m could be observed. Combining this with informationof other gas-phase atoms, molecular lines, PAHs, silicates, and ices put H2 intoperspective with the other constituents of the ISM.There is no known efficient gas-phase formation mechanism for H2 at low

temperatures and at the densities of the ISM. It is believed that H2 is formed ondust particles, but the detailed formation mechanisms are not known because ofthe limited amount of knowledge about dust particles.To account for the observed amounts of H2, very effective means for its produc-

tion at low temperatures (<30 K) are needed. Models exist whereby H2 is formed onsurfaces of PAHs or on surfaces of very small grains. Several scientists have arguedthat the surface roughness of particles plays an important role.The formation of molecules more complex than H2 has also been studied. The

mechanisms include various combinations of molecule building in the gaseousphase or on grain surfaces, sometimes with the aid of UV radiation, which, bycharging grain surface, can enhance molecule formation.


2.6.4.3 Formation of CO and H2OAfter H and He, the most common elements in the Universe are O and C. Both COand H2O form readily in gaseous form, possibly in the strong stellar winds duringthe giant phase of stellar evolution. The reservoir of atomic C, which is smallerthan that of O, is nearly depleted in forming CO.The reactions in forming H2O from H and O are among the most exothermic

ones. H or H2 become ionized and react to form H3+. This reacts with atomic O to

form HO+ and H2 as well as H2O+ and H. The ions HO+ and H2O+ react with freeelectrons to form H2O and OH radicals. Thermally, the water molecule is stableuntil a temperature of 3 000 K. This is an important aspect in considering theorigin of Earth’s oceans. H2O can also form directly on grain surfaces.

2.7Generation of Stars: Formation of the Sun and Planets

The formation of a stellar system starts with the collapse of a local dense part of aGMC, the same regions where the most complicated molecules are found. First thedensity increases and central parts of the condensation heat up. The condensation,which is still starless, acquires a higher angular velocity in the center of the densityenhancement. The collapsing system settles into a disk-like geometry. Both thehigher angular velocity at the center and the settling into a disk are due to theconservation of angular momentum. Such dusty disks are seen, for example, in theOrion Molecular Cloud (OMC). They are so dense that even IR does not penetratethrough them, as they appear as dark ellipses of circles against a brighter IRbackground.Some of these “propylads” have a bright star in the center. They have entered an

evolutionary phase at which the condensation in the center has reached a highenough temperature and density that it has turned into a new star. As the starbegins to shine, it will start to ionize H gas around it and a HII region will form. Ifthe newly born stars are located at the edge of the cloud, as inM42, one can note thetypical emission line spectrum, as the tenuous gas emits at a few characteristicwavelengths only. From the spectra one can calculate, among other things, thetemperature and the density of the gas in these HII regions.

2.7.1Accretion Disk of the Sun

When the first generation of normal stars was produced, the building blocks forplanets were not readily available. As we will see later, we need ices and rocks toform planets.It is important to note that the heavier elements C, N, O, Si, and Fe, which are

needed for the planetary building blocks, were produced by nuclear fusions in thefirst generation of normal stars and further processed by the subsequent molecularevolution in the ISM.


Our Sun and its accretion disk formed in a molecular cloud that was enriched byheavier elements from the first generation of normal stars. Traces of the cloudfrom which our Solar System was formed can be found in meteoritic dust in ourSolar System, e.g., in the form of Al2O3, diamonds, graphite, and SiC within the“fine-grained” matrix in the most pristine chondrite class meteorites.The material that would finally form the stars and planets formed a disk similar

to the ones seen in the OMC. This disk initially consisted of H and He, but all otherelements were also present, as were molecules similar to the ones observed at radiowavelengths in molecular clouds. All the matter began falling towards the centralplane of the disk. The dust grains, both ice-coated and iceless, sedimented to acommon central plane that was to become the general plane of orbits and equatorsof the planets and the Sun. The time it took for the embryonic Solar System toachieve that phase was about one million years.How the planets formed goes along the following line of thought: small dust

particles started to stick together and they grew fairly rapidly into meter-sizeaggregates. Because the aggregates were on similar orbits, their relative velocitieswere small and thus collisions occurred at low-velocity differences. These aggre-gates grew to larger sizes, and once they reached about 1 km, gravitation startedcompacting them. In a few ten thousand years the 1-km particles grew into1000-km planetesimals. At this point they were already so large that the gravitystarted to act on their shape making them round.The speed of the planet formation processes following next can be estimated by

observing dusty disks around solar-type stars of different ages and by correlatingthe age of the star with the state of the disk. For a solar-type star, a planet-formingdisk, the protoplanetary disk, disappears in about 7 million years. After that time,no substantial amount of gas and dust is available for planet formation, althoughdebris disks can last for 400 million years. Somematter remains even for billions ofyears (e.g., zodiacal light and Kuiper Belt objects). Modeling of disks gives similartimescales.Models can provide a temperature profile of the disk. The general temperature

profiles are dependent on the distance from the central star, usually r–0.75 to r–1. Innormal air pressure, H2O would crystallize into ice at 273 K. In space, where H2Osublimates from the solid phase directly into the gas phase, the sublimation pointcan be as low as about 150 K. Beyond some distance from the star, at the so-calledsnow line, H2O ice stays in a solid phase. Inside the snow line, H2O ice sublimatesinto the gas phase. One experimental way to estimate this distance is to study thecrystallization temperatures of meteorites, as done by Chris McKay. The separationof ordinary chondrites and carbonaceous chondrites took place at temperatures of450 K. If the carbonaceous chondrites are identified with the C asteroids and theordinary chondrites with the S asteroids, then one can place a rough distance forthe temperature of 450 K at 2.6 AU. This would now set the snow line at some-where between about 5 AU and 15 AU. The inner parts of the disk were hot,implying that ices melted and evaporated. The temperature estimate for theaccretion disk at 1 AU distance from the above models would be about 500–1200 K. Clearly, at these temperatures the newly formed Earth was hot, with no

2.7 Generation of Stars: Formation of the Sun and Planets 45

water or other volatiles and no atmosphere at the beginning, and was indeed a veryinhospitable place for life. Some protoplanetary disk models suggest a flattertemperature profile and a snow line closer to the Sun, but in general, there isreasonable agreement that the snow line was at about 5 AU.In the inner part of the Solar System, rocky planets were formed. The last

impacts in the planetary accretion were often from nearly similar-size objectsand were quite severe for the final planet. Examples are the Moon-forming impacton Earth, the impact that possibly caused the retrograde spin of Venus, and themantle-destroying impact on Mercury.In the outer parts of the Solar System, beyond the snow line, different processes

took place. There was more solid material around in the form of (mainly H2O) ice.Once the core of Jupiter had grown to about 20 Earth masses, its gravitationbecame large enough even to hold H and He after capturing them. A runawayaccretion took place, whereby Jupiter started to grow rapidly. With its increasedsphere of influence, it grew even larger until all the available matter in its vicinitywas consumed. A similar process also took place with Saturn, Uranus, andNeptune. Beyond the orbit of Neptune, a large number of icy objects were left.These are now known as Kuiper Belt objects. Several 1000-km objects have beendetected in the last 10 years, some of them of the larger than the dwarf planet Pluto.The large gravitational fields of the outer planets affected the dynamics of the

remaining boulders, both the icy ones, the comets, and the iceless ones, theasteroids. Some of these were ejected from the Solar System and others wereslingshot into the inner parts of the Solar System. This had two effects. First,comets and asteroids were cleared from the vicinity of the giant planets, andsecond, the inner planets experienced a shorter, more intensive heavy bombard-ment of asteroids and comets. Comets and asteroids were important in deliveringthe ingredients necessary for life (see Chapter 3).

2.7.2Formation of the Earth

When did the Earth form? Relative abundances of isotopes of various elements inpristine chondrites can be used to determine the age of our Solar System. Thisgives an age of 4.567 € 0.002 billion years, which defines the moment when thetemperature of the chondrites cooled enough for the minerals to crystallize. Theaccretion continued for the next 100 million years. The size of large impactsincreased until the last one, which stripped the protoatmosphere and possiblymelted the whole Earth. This took place about 4.45 billion years ago, as measuredby xenon isotope ratios of the atmosphere. The Moon-forming impact was earlier,possibly some 4.52 billion years ago. It was thought to be a grazing impact ofa Mars-size body. Because of the impact, both bodies melted and the coresmerged to form the core of the Earth. Part of the debris that was ejected intospace appears to have formed the Moon. The first landmasses formed quite earlyon Earth. Zircon crystals collected from the Jack Hills region in western Australiaindicate that granitic crust formed as early as 4.42 billion years ago. One can


consider that the formation of the Earth ended at this time, although evenpresently the mass of Earth increases by about 20 000 tons per year due to thefall of micrometerorites.At the beginning, the Earth was so hot that its surface was covered by molten

magma, which means a magma ocean (liquid rock!). The acquired atmosphere wassaturated and contained hot H2O vapor, N2, and most likely CO2 and H2. Atpresent, this is our best guess for the atmospheric composition. It is doubtfulthat any measurements will be able to determine the exact constituents of theearliest atmosphere. Note that the Earth experienced a strong greenhouse effect ofabout 2 000 K because of high amounts of both CO2 and especially H2O. The totalpressure of the atmosphere at the surface was about 1000 times the present value.H2 was such a light molecule that Earth was not able to hold it for a long time. TheEarth started to cool by IR radiation. Once the atmosphere cooled to the dew pointof about 200 �C, a long rain began. Most of the H2O vapor in the atmosphere rained.The oceans had formed. The water was still hot, the water was fresh, and themantle below the sea was also hot. The Earth was left with a CO2 and N2

atmosphere.Volcanic activity was high, and volcano islands formed. The hot magma miner-

als, such as peridotite, interacted with water and formed minerals containingcrystal water, e.g., serpentinite. These mineral formations grew larger. They gainedweight and collapsed, sinking into the mantle. These hydrated minerals experi-enced a partial melting at relatively low pressures and temperatures, formingtonalities among others. They were now lighter than the basaltic seafloor andstarted “floating” on it, eventually becoming the main ingredient for continents. Asrocks started to protrude from the ocean, erosion set in. Under high temperatureand high CO2 partial pressure, erosion was enormous, with an estimated rate ofabout one million times the present value. The CO2 dissolved into water, creatingcarbonic acid H2CO3. This reacted with wollastonite (CaSiO3), changing it intocarbonates (CaCO3) and quartz (SiO2). The carbonates sedimented onto the oceanfloor. This was an effective means for removing CO2 from the atmosphere.

2.7.3Early Rain of Meteorites, Comets, Asteroids, and Prebiotic Molecules

The scars of the heavy bombardment of the inner planets by asteroids and cometscan be seen on the “face” of the full Moon. The maria are lava-filled impact cratersof gigantic proportions. Similar impacts took place on Earth about 23 times moreoften than on the Moon. Some of those impacts had enough energy to evaporatethe oceans.Asteroids and comets still abound. Asteroids can be described as large chunks

(10–1000 km) of rocks made of darker and lighter materials. The brightness of anasteroid depends on the geometric effects of the asteroid’s distance from the Sunand its reflectivity or albedo. The short-term light variations that are seen areusually due to rotation only. Comets are large chunks of a mix of clay, ice, and sand.As they approach the Sun on their elliptical orbits, most of them develop a coma


and some also a noticeable dust and/or ion tail. In addition to geometric androtational effects, brightness variations due to some kind of activity of volatilematerials, such as H2O, CO, are often observed.Meteorites, which are small pieces of asteroid material surviving the reentry to

Earth, have been critical for understanding asteroids, as they have been historicallythe only means to study these celestial bodies. Radio astronomical spectroscopyopened a new window for cometary molecular studies in the 1970 s, and recentspace missions have provided pictures, onsite measurements, and (still unpub-lished) sample returns from these bodies. The study of these bodies is of theutmost importance for understanding the evolution of the Earth and the delivery ofprebiotic molecules to the Earth and other bodies in our Solar System. One has tobear in mind that although comets and asteroids are quite pristine in manyrespects, most of those bodies have been orbiting our Sun for the last 4.567 billionyears and most likely experienced at least some evolution.While asteroids and comets brought global and local destruction to the early

Earth, they brought at the same time key ingredients for building our present Earthand possibly the critical prebiotic molecules for the origin of life.Asteroids and comets are roughly of the same size. It is thought that the main

cause for the difference between these two groups is the site of their formation.Asteroids formed inside the snow line and comets outside of it. Asteroids shouldhave relatively little H2O, while comets should have a significant portion of solidH2O. The distinction between these two groups is not sharp because there aremany objects that are intermediate in character, but roughly speaking, the classi-fication is valid. Most of the known asteroids are concentrated in orbits betweenMars and Jupiter, while most comets have orbits extending far beyond Neptune.The composition of asteroids has been inferred mainly from studies of meteor-

ites. No onsite measurements exist. Several asteroids have been photographed byflyby space probes, so there is some idea of what they look like and what their colorsand albedos are like. This is of great importance in understanding, for example, themodeling of asteroids based on their brightness variations.Meteorites come in three main types: iron, iron-stony, and stony. Iron meteorites

are nearly solid iron-nickel. Stony meteorites usually contain minerals such asolivine and pyroxene and relatively small amounts of iron. The latter are furtherdivided into chondrites and achondrites. The latter are thought to originate fromthe Moon or Mars (see Chapter 8). About 80% of all recovered meteorites arechondrites. These have small chondrules, which are considered to be the originalmolten material that crystallized during the formation of the meteorites. They arethe oldest rocks in our Solar System. Five percent of chondrites are classified intocarbonaceous chondrites, due to their elemental C.If asteroids are assumed to be made of matter similar to meteorites, then it is

quite clear that asteroids delivered iron and nickel and vast quantities of silicates tothe Earth. C is an important ingredient in many meteorites (up to 4%), as is H2O(20% in meteorites). The asteroid Ceres appears to have 25% H2O by mass, whichis more freshwater than found on Earth. The supply of these raw materials wasmore than sufficient for delivering the quantities found presently in silicates


(continents) and carbon (biosphere). Also, a significant portion of H2O (oceans)may have arrived through asteroids.The outgassing of volatiles in comets has been studied mainly by radio and IR

spectroscopy. Several dozen molecules have been detected, among them H2O,HCN, H2CO, CH4, which all are important ingredients for the origin of life. Recentobservations from the Stardust return mission to Comet Wild 2 revealed that atleast this comet contains particles from the presolar GMC, from the protosolardisk, and also from later reprocessed matter.The Murchison meteorite fell in Australia in 1969 and was almost immediately

collected. It carries a large number – about 70 – amino acids, as well as nucleotides,sugars, and other organic molecules (see Chapter 3). Hence, the ingredients for lifecan be found in our vicinity in space, and this matter is seen falling even nowadays,as shooting stars. One can easily argue that this would be the easiest means forproviding the young Earth with the seeds for life, maybe not in the form of self-destructing shooting stars but rather in the form of lightly floating micrometeor-ites.Comets also contain N-bearing ices. Because the newly born Earth was free of

volatiles, it seems that comets were the delivery mechanism for N2, the maincomponent of our present atmosphere. The secondmost abundant component, O2,appeared in the atmosphere much later about 2.2 billion years ago, when cyano-bacteria started to produce it – maybe – as a waste product of photosynthesis.

2.7.4D/H Ratio and Oceans

The oceans cover about 70% of the surface of the present Earth. Our planet is oftenreferred to as the “blue planet.” If the whole planet is considered, only 0.04% of themass is in the oceans. Still, the question of oceans is an important one becausewater has played an important role in the origin and evolution of life (seeChapter 1).Asteroids and comets delivered H2O and other volatiles to the young Earth.

These volatiles did not have enough time to evaporate significantly, because theasteroids and comets plunged to the inner Solar System from the vicinity of thesnow line or from far beyond it. Alternatively, it has been suggested that asignificant fraction of the H2O originated from H2O within the accretion disk,but it is not clear how this oxygenation of H could proceed in a relatively hotgaseous disk. However, gaseous H2O formed in the protosolar disk could endure,in principle, temperatures up to 3 500 K in the gas phase. Some geologists havesuggested that H2O was trapped in the minerals that formed the Earth and thatH2O was later outgassed by the hot mantle. One argument that has been raisedagainst the cometary origin of water is the deuterium (D) to H ratio (D/H) of H2O.The standard terrestrial reference in geology for the D/H ratio is the

Vienna Standard Mean Ocean Water (V-SMOW), which has a value ofD/H = (155.76 € 0.05) � 10–6. In interstellar molecular hydrogen, the D/H ratio isabout 15 � 10–6: this is the cosmic D/H ratio. Some cold interstellar molecules,


however, show a large D/H enrichment, with water having HDO/H2O showing anenrichment of a factor of 20–40 or a D/H of 300–600 � 10–6 and DCN/HCN havingan enrichment of up to a factor of 1000 to the cosmic D/H ratio.The first cometary value wasmeasured by theGiottomission for Comet Halley as

HDO/H2O = (330 € 20) � 10–6. This value was in line with what was seen in waterfrom cold interstellar clouds, suggesting that the water in Comet P/Halley waspresolar.This cometary value created a problem in that the oceanic D/H ratio was too low

by a factor of about 2 to be explained by a cometary origin if Halley represented atypical value for a comet. The concept of a “D/H problem” was created. The nextcomets to be measured for the HDO/H2O ratio were Comet C/1995 O1 Hale-Boppand Hyakutake. The relative abundances measured, (330 € 80) � 10–6 and(280 € 40) � 10–6, respectively, were in line with Comet Halley. The controversybetween cometary HDO and oceanic HDO appeared to grow stronger.One can also turn to other planets in our Solar System. The two giant planets

have low D/H ratios: a value of (16 € 3) � 10–6 for Jupiter and of (18 € 5) � 10–6 forSaturn was measured by IRTF telescope, located on top of Hawaii’s toweringvolcano Mauna Kea. They are both close to the cosmic abundance and in agree-ment with the HDO/H2O ratios of the comets. Uranus and Neptune appear to havea higher value, at about D/H = 60 � 10–6. The Huygens mission (see Chapter 9)measured the D/H ratio for Titan, yielding a fractional abundance of(250 € 50) � 10–6. To complete the known HDO/H2O ratios, Mars has a D/H ratioof (810 € 30) � 10–6 or about 5 SMOW, and Venus has a staggering ratio of(25 € 5) � 10–3or 160 € 32 SMOW. Carbonaceous chondrites show typical valuesof 130–170 � 10–6, close to the SMOW value. On Mars and Venus the loss of lighthydrogen can be understood by its escape into space. Titan’s D/H values are notwell understood yet.As noted, the D/H ratio in the Solar System varies considerably, depending on

whether proper D/H is considered or HDO/H2O is measured. If one considers oneof the two types of measurements only, then the variation remains still large ineach type.With a preconceived presumption that the D/H ratios measured in the three

comets mentioned above, namely, Halley, Hale-Bopp, and Hyakutake, are repre-sentative of the comet population that formed Earth’s oceans, and if the D/H ratiosmeasured in the comets and in the seawater represent the D/H at the time offormation of the oceans, then one has a “D/H problem.” In this scenario, Earth’swater came partially from comets and partially from the water vapor bound tograins in the accretion disk.The story does not end here. The HDO/H2O ratio of the comet C/2004 (Mach-

holz) yielded an upper limit of 230 � 10–6 (3�), obviously below the value from othercomets. HDOwas also detected in comet C/2001 Q4 (NEAT), but no value has beenpublished so far for the D/H ratio. Recent observations of the comet C/1999 S4(LINEAR) suggest that this comet has a very different chemistry than comets suchas Halley, Hyakutake, or Hale-Bopp, which have chemistry consistent with theirformation being beyond the orbit of Neptune. The detailed analysis of the abun-


dances of molecules in comet C/1999 S4 (LINEAR) by Mumma suggests that thiscomet may have formed in the Jupiter–Saturn region, close to the ice line. In thisregion the D/H ratio could have been significantly lower than in the colder spacebeyond Neptune. The delivery of water from these comets could explain the D/H ofthe terrestrial oceans.Finally, the recent Deep Impact mission to Comet Temple and the Stardust

sample return mission from Comet Wild 2 have raised questions of whether thecomets can undergo substantial evolution during their lifetime and whether thesurface of the comet represents the conditions inside the core.

2.8Further Reading

2.8.1Books or Articles in Books

Despois, D., Biver, N., Bockl�e-Morvan, D.,Crovisier, J. Observations of molecules incomets, in: D. C.Lis, G. A. Blake, E. Herbst(Eds.) Astrochemistry – Recent Successes andCurrent Challenges, IAU Symp 231, pp.19–128, 2005.

Irvine, W.M., Schloerb, F. P., Crovisier, J.,Fegley, B. Jr., Mumma, M. J. Comets: A linkbetween interstellar and nebular chemistryin: V. Mannings, A. P. Boss, S. S. Russell(Eds.) Protostars and Planets IV, University ofArizona Press, pp. 1159–1200, 2000.

Karttunen, H., Krçger, P., Oja, H., Poutanen,M., Donner, K. J. (Eds.), Fundamental As-tronomy, 4th ed., Springer, Berlin, Heidel-berg, New York, 2003 (a good comprehen-sive book for astronomy).

Thomas, P. J., Chyba, Hicks, R. D., C. F.,McKay, C. P. (Eds.) Comets and the Originand Evolution of Life, 2nd ed., Springer, Ber-lin, Heidelberg, New York, 2006.



Abe, Y. Physical state of the very early Earth,Lithos 1993, 30, 223–235.

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de Bergh, C. The D/H ratio and the evolutionof water in the terrestrial planets, Origin LifeEvol. Biosphere 1993, 23, 11–21.

Bockel�e-Morvan, D., Gautier, D., Lis, D. C.,Young, K., Keene, J., Phillips, T., Owen,T., Crovisier, J., Goldsmith, P. F., Bergin,E. A., Despois, D., Wotten, A., Deuteriumwater in Comet C/1996 B2 (Hyakutake) andits implications for the origin of comets,Icarus 1998, 133, 147–162.

Ceccarelli, C., Dominik, C., Caux, E., Lefloch,B., Caselli, P. Detection of deuterated waterin a young proto-planetary disks, in:D. C.Lis, G. A. Blake, E. Herbst (Eds.) Astro-chemistry –Recent Successes and CurrentChallenges, IAU Symp 231, 2005 (abstract)

Cernicharo, J., Crovisier, J. Water in space: Thewater world of ISO, Space Sci. Rev. 2005, 119,29–69.

Charnley, S. B., Rodgers, S. D., Butner, H.M.,Ehrenfreund, P. Astro-ph/0204381 2002(14 pages).

Cuppen, H.M., Herbst, E. Monte Carlo simu-lations of H2 formation on grains of varyingsurface roughness, Mon. Not. R. Astron. Soc.2005, 361, 565–576.

Dartois, E. The ice survey opportunity of ISO,Space Sci. Rev. 2005, 119, 293–310.

Dietrich, M., Wilhelm-Erkens, U. Elementalabundances of high redshift quasars, Astron.Astrophys. 2000, 354, 17–27.

Donahue, T.M. Evolution of water reservoirson Mars from D/H ratios in the atmosphereand crust, Nature 1995, 374, 432–434.

Grinspoon, D.H. Implications of the high D/Hratio for the sources of water in Venus’ at-mosphere, Nature 1993, 363, 428–431.

Habart, E., Walmsley, M., Verstraete, L.,Cazaux, S., Maiolino, R., Cox, P., Boulanger,F., Pineau des ForÞts, G. Molecular Hydro-gen, Space Sci. Rev. 2005, 119, 71–91.

Henning, K. Molecular formation in interstel-lar clouds by gas phase reactions, Astron.Astrophys. Suppl. S. 1981, 44, 405–435.

Hornekaer, L., Baurichter, A., Petrunin, V. V.,Field, D., Luntz, A. C. Importance of surfacemorphology in interstellar H2 formation,Science 2003, 302, 1943–1946.

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2.9 Questions for Students 53

2.8.3Web Sites

NASA page on stars and galaxies:http://www.nasa.gov/vision/Universe/starsga-

laxies/index.htmlWilkinson Microwave Anisotropy Probe

(WMAP) page, a NASA Explorer missionmeasuring the temperature of the comicbackground radiation:

http://map.gsfc.nasa.gov/European Southern Observatory:http://www.eso.org/Al Wootten’s page – including a list of known

ISM molecules:http://www.cv.nrao.edu/~awootten/Cologne database on molecular spectroscopy:http://www.ph1.uni-koeln.de/vorhersagen/

main.html

UC San Diego page about ISM:http://cassfos02.ucsd.edu/public/tutorial/

ISM.htmlISO telescope:http://sci.esa.int/science-e/www/object/index.

cfm?fobjectid=32721Near Earth Object program:http://neo.jpl.nasa.gov/Dave Jewitt’s Kuiper belt page:http://www.ifa.hawaii.edu/faculty/jewitt/

kb.htmlUC Berkley geology page:http://www.ucmp.berkeley.edu/exhibit/geolo-

gy.html

2.9Questions for Students

Question 2.1Consider the Si atom in the SiO2 molecule in your porcelain coffee cup and the C

atom in the tiny sugar crystal inside your coffee cup, just before you pour your hotcoffee on it. Where were these atoms formed? How did their long way into yourcoffee cup differ from each other?Question 2.2At any given moment, there are about ten 10-meter meteoroids/asteroids in

Earth’s vicinity, at a distance that is smaller than the Moon’s distance from Earth.Assuming a typical velocity of 10 km s–1, make a rough calculation of how long

should it take for such an object to hit the Earth. What is the energy liberated insuch an impact? Compare it with something sensible. Compare the mass flux fromthis hypothetical impact with the mass flux from micrometeorites.Question 2.3The triple-alpha reaction is a critical step in the formation of C, and thus in the

formation of life. Find other cosmic steps that have turned out to be critical forgetting together all the important ingredients for life on Earth.Question 2.4Interstellar molecules are observed in gaseous and solid phases. What are the

differences between these groups? Which of the differences are real and which aredue to limitations in observing techniques or due to limiting factors caused by theatmosphere?


3Basic Prebiotic ChemistryHerv� Cottin

This chapter is devoted to the study of prebiotic chemistry. Itfocuses on the abiotic synthesis of key prebiotic compounds –amino acids, purine and pyrimidine bases, and sugars – fromsimple molecules, such as methane (CH4), hydrogen cyanide(HCN), and formaldehyde (H2CO), thereby filling the gap betweenchemistry and biology. In the first section living systems aredismantled into more elemental fragments: organic molecules. Toaddress the origin of life, the next question is how those fragmentscan be synthesized in an abiotic manner. After a short historicalreview, different tracks of prebiotic chemical evolution are ex-plored: an endogenous production of the molecules of life withinearly Earth’s atmosphere or in the depths of primitive oceans, or anexogenous source of prebiotic molecules through space delivery viameteorites and comets. The last section describes chemical path-ways of the synthesis of the building blocks of life.

3.1Key Molecules of Life

Life as we know it is based on a complex chemistry involving highly sophisticatedbiological molecules such as proteins, ribonucleic acids (RNA), or deoxyribonucleicacids (DNA). Such elaborated structures result from a complex chemical evolution,starting with the simplest organic compounds. At some point, at an as yetundefined stage of complexity and organization of matter, an important step ismade and chemistry turns into biology.

3.1 Key Molecules of Life 55


3.1.1Dismantling the Robots

In Chapter 1 Andr� Brack compares the premises of an emerging life to parts of“chemical robots,” which make copies of themselves and are capable of evolutionthrough “mistakes” during reproduction. Following this idea, life could be consid-ered as any type of structure (at a molecular or cellular level or any other form) withsome complexity that bears information to make the robot work and that makescopies of itself. From time to time, the copy would not be the exact image of itsoriginal. This modified copy could be either more adapted to the environment thanits original or less adapted, and therefore either more or less favored to survive.Then it would make more copies of its new model with either more or lessefficiency.Whereas it is quite difficult to find a proper general definition of life (see Chapter

1), it is much easier to answer the question “What is life made of?” The answerturns out to be surprisingly simple. If one considers all living systems on Earth,from unicellular systems such as bacteria to multicellular systems such as plantsand animals, they are all built from the same basic components.Each living system is made of at least one cell. A cell can in turn be broken down

into more elemental parts: proteins, RNA, and DNA molecules embedded withinthe membrane of the cell. These biomolecules are made of mainly the followingelements: carbon (C), hydrogen (H), oxygen (O), and nitrogen (N). The membraneis built from long organic amphiphile chains. These chains possess a polar head,which makes them soluble in water (hydrophilic part of the molecule), and anapolar tail, which is insoluble in water (hydrophobic part of the molecule). Suchmolecules are called amphiphiles (amphi = both), because they consist of both ahydrophobic and a hydrophilic part. These amphiphile structures may self-organ-ize into vesicles (Fig. 3.1).Inside the cell, which is surrounded by the membrane, a complex molecular

engine is working (Fig. 3.2). But, from a simplified chemical point of view, theinterior of the cell turns out to be made of mainly proteins and nucleic acids, suchas DNA and RNA. Of course, there is a wide range of proteins that play various key

3 Basic Prebiotic Chemistry56

Fig. 3.1 Long organic amphiphile chains with a polar head thatmakes them soluble in water and a water-insoluble apolar tail(left), which may self-organize into vesicles (right).

roles in metabolism and an enormous diversity of DNA and RNAmolecules, whichis reflected by the large diversity of living forms on Earth. But this diversity resultsfrom a combination of 28 molecules only. Every known living organism could becompared with a Lego construction with 28 different kinds of bricks: 20 aminoacids to build the proteins, five purine or pyrimidine bases, two sugars, and onephosphate bridge to build DNA and RNA. The following main functions can beattributed to the three families of molecules:

• DNA stores information,• RNA transmits information, and• proteins act as catalysts.

Table 3.1 shows the basic composition of a cell exemplified by the bacteriumEscherichia coli.


Fig. 3.2 Basic cellular components (DNA, RNA, and proteins)and functions (storage and transfer of information and proteinsynthesis in the ribosomes).

Table 3.1 Composition of a bacterial cell as exemplified byEscherichia coli.

Component Percentage of totalcellular weight

Molecular mass(g mol–1)[a]

Water 70 18Proteins 15 40 000RNA 6 ~ 106

DNA 1 2.5 � 109

Carbohydrates and precursors[b] 3 150Lipids and precursors[b] 2 750Amino acids and precursors 0.4 120Nucleotides and precursors 0.4 300Others[c] 2 –

a Averaged in a mixtureb Parts of the cell membranec Other small molecules and inorganic ions

3.1.2Proteins and Amino Acids

Proteins are organic compounds built from a succession of amino acids linkedtogether by peptide bonds. Proteins can play different roles: some are of importanceat a structural level in the cells, while others are enzymes that act as catalysts forchemical reactions. Their properties result from their chemical formula and fromtheir spatial conformation (how the amino acid chain organizes itself in space).An amino acid is a molecule that contains both an amino group (-NH2) and a

carboxylic acid (-COOH) function (Fig. 3.3). If the carbon that bears the amino


Fig. 3.3 (a) General formulaof an Æ-amino acid; R repre-sents different side chains; (b)glycine; (c) 3-dimensionalpresentation of an Æ-aminoacid (alanine) with an asym-metric carbon (marked witha star). Note that these mole-cules, which have an identicalmolecular formula, cannot besuperimposed one over theother.


Fig. 3.4 The 20 biological amino acids; association of severalamino acids through peptide bonds produces a polypeptide.

group is the same as the one bearing the carboxylic function, then the amino acid iscalled an Æ-amino acid. If the amino group is linked to a carbon that is one C awayfrom the carbon bearing the carboxylic function, then the amino acid is called a�-amino acid, and so forth.The general structure of an Æ-amino acid is shown in Fig. 3.3 a. R represents a side

chain specific to each amino acid. In only the simplest amino acid, glycine, is the R-group hydrogen (Fig. 3.3 b). For all other Æ-amino acids, R is different from H. Inthat case the central carbon atomhas four different substituents and is then called anasymmetrical carbon. As shown in Fig. 3.3 c, two spatial arrangements (configu-rations) of these substituents are possible, resulting in two different molecules(called enantiomers) that are mirror images of each other. Molecules with anasymmetric or chiral C atom affect the orientation of polarized light when it passesthrough a sample of molecules of one configuration. Configuration 1 shifts theorientation of polarized light to the right (dextrorotary), while configuration 2 wouldshift it to the left (levorotary). These two configurations of amino acids are called L orD (L-compounds rotate the plane of polarized light to the left, D-compounds to theright). A mixture of equal quantities of both configurations is called a racemicmixture. It neutralizes the effect, and polarized light passes unchanged. Thisproperty toward polarized light has no direct effect on life, but the configurationof amino acid (D or L) is extremely important for the spatial orientation (conforma-tion) of long chains of amino acids: the proteins. The properties of proteins aredirectly linked to their conformation, and they have different characteristics if builtfrom L-amino acids, D-amino acids, or a mixture of both (see also Chapter 1).Asmentioned above, in the proteins the amino acids are linked by peptide bonds.

Peptide bond formation is a condensation reaction leading to the polymerization ofamino acids into peptides and proteins with the concomitant elimination of water(Fig. 3.4). Peptides are small, consisting of a few amino acids. Proteins are poly-peptides of greatly divergent length.To build the proteins, life uses a combination of only 20 amino acids (Fig. 3.4), all

of which appear in one enantiomer: the L-form. Why L-enantiomers were selectedover D-enantiomers remains unknown, but this is a property shared by all livingsystems (with a few exceptions in the bacterial domain; see Chapter 5).

3.1.3DNA, RNA, and Their Building Blocks

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are long-chained organicmolecules that contain genetic code information (see Chapter 4). From a chemicalpoint of view, in terms of building blocks of life, their composition and structurecan be quite simply explained.The backbone of DNA and RNA is a succession of sugars (deoxyribose for DNA,

ribose for RNA) linked by phosphate bridges (PO42–) (Fig. 3.5). The “letters” of the

genetic code, which are connected to each sugar molecule, are the purine basesadenine (A) and guanine (G) and the pyrimidine bases cytosine (C), thymine (T) (Tin DNA only), and uracil (U) (in RNA only) (Fig. 3.6). The association of the sugar


with one of the bases is called a nucleoside. If a phosphate is linked to a nucleoside,the resulting structure is called a nucleotide. The polynucleotide is named accord-ing to the sugar in its structure: DNA if the sugar is a deoxyribose, and RNA if thesugar is a ribose.


Fig. 3.5 Structure of DNA. DNA and RNA are linked chainsof nucleotides, each consisting of a sugar, a phosphate, andone of the five nucleobases (purine bases: adenine and guanine;pyrimidine bases: cytosine and thymine in DNA or cytosine anduracil in RNA)


Fig. 3.6 Chemical structure of DNA and RNA nucleotides. Thedifference between the two types of molecules is the substitutionof one H (DNA) by OH (RNA) on the sugar and thymine (DNA)by uracil (RNA).

The genetic code is encrypted in the specific succession of purine and pyrimidinebases. It contains information about which succession of amino acids is to be builtin which proteins (see Chapter 4). This information is transferred to the ribosomes,the “proteins factory,” via RNA (Fig. 3.2). Ribosomes are composed of RNA andproteins.All living systems function according to this very same mechanism. What makes

a mouse different from an elephant or a mushroom is the number and successionof the “letters” in the DNA molecules.DNA and RNA are usually seen as carriers of genetic information. This picture

has changed with the discovery of the self-splicing of certain RNAs. These obser-vations laid the foundation for the concept of catalytic RNA, the ribozymes (seeChapter 4). This catalytic capacity of RNA led to the idea of the RNA world thatmight have preceded life as we know it today: a simplified cellular biochemicalmachinery in which RNA plays all roles that are essential for life; it carries andtransmits information, and it catalyzes the reactions.

3.1.4First “Prebiotic Robot”

For building the first “prebiotic robot,” and then the first living system, thefollowing compounds must be available:

• long organic amphiphile chains for building membranes;• amino acids for building proteins;• phosphate for the backbone of nucleic acids;• purine and pyrimidine bases as “letters” for the genetic code

in DNA and/or RNA; and• sugars for the nucleic acids (ribose in the RNAworld scenario).

These molecules need to be synthesized under prebiotic conditions, either on earlyEarth or in space. Of course, the presence of the building blocks for life is notsufficient to make the first prebiotic robot; however, they are prerequisites in thescenario of the origin of life.

3.2Historical Milestones

The building blocks of life have been discovered and characterized since the early19th century (Table 3.2). In these early times, the question of the abiotic synthesis ofsuch molecules in the test tube seemed far beyond the scope of most of thechemists’ capabilities. Moreover, it was not even considered as a question ofinterest. It was the generally accepted opinion that organicmolecules are the resultof the activity of organized, i.e., living, systems, and are associated with amysterious“vital energy.” In 1827, the Swedish chemist Jçns Jacob Berzelius (Fig. 3.7) wrote,“Art cannot combine the elements of inorganic matter in the manner of living

3.2 Historical Milestones 63

nature.” (Berzelius also invented the words “polymerization,” “catalysis,” “electro-negative,” and “electropositive” and discovered the elements selenium [Se], silicon[Si], and titanium [Ti]). At that time, there was no way known to synthesize organicmolecules in the laboratory, and no reason to look for such ways.

Table 3.2 Milestones in the discovery and characterization ofimportant biochemical monomers or polymers.

Year Discoverer Monomer/polymer

1810 W.H. Wollatson Cystine[a]

1819 J.L. Proust Leucine[a]

1823 M.E. Chevreul Fatty acids1838 J.J. Berzelius Proteins1869 F. Miescher DNA1882 A. Kossel Guanine1883 A. Kossel and A. Neumann Thymine1886 A. Kossel and A. Neumann Adenine1894 A. Kossel and A. Neumann Cytosine1900 A. Ascoli Uracil1909 P.T. Levene and W. A. Javok Desoxyribose1906–1936 P.T. Levene et al. Ribose, ribonucleotides

Source: Adapted from Miller and Lazcano 2002.a Amino acid

A firm denial to this theory was brought in 1828 by Berzelius’ friend and formerstudent Friedrich Wçhler (Fig. 3.7). This German chemist succeeded in the firstabiotic synthesis of an organic molecule, urea (NH2-CO-NH2), “without the need ofan animal kidney,” as he said at the time, by simple heating of ammonium cyanate(NH4OCN). From then on, a breach was made in the “vital energy” theory, and,slowly, organic chemistry became the chemistry of carbon-based molecules.


Fig. 3.7 Famous chemists of the 19th century. From leftto right: Jçns Jacob Berzelius (1779–1848), Friedrich Wçhler(1800–1882), Adolph Strecker (1822–1871), and AlexandrButlerov (1828–1886).

Soon after this pioneering finding, the synthesis of other organic compoundswas realized. Regarding the synthesis of molecules of prime interest to the origin oflife, two major achievements shall be pointed out. In 1850, Adolf Strecker (Fig. 3.7)succeeded in the first laboratory synthesis of an amino acid: alanine from amixtureof acetaldehyde (CH3CHO), ammonia (NH3), and hydrogen cyanide (HCN). A fewyears later, in 1861, Alexandr Butlerov (Fig. 3.7) performed the first laboratorysynthesis of sugar mixtures (also known as the formose reaction) from formaldehyde(HCHO) using a strong alkaline catalyst (NaOH) (see Section 3.4.3).Although these discoveries were very interesting, they were not linked to the

origin-of-life problem. Hence, little progress was made in finding a scientificdescription of the origin of life. One had to wait until 1924 for the publication ofthe book Origin of Life by Aleksandr Ivanovich Oparin (1894–1980). Oparin intro-duced the concept of chemical evolution, which could be seen as the roots of theDarwinian tree of evolution. In this concept, life was the result of a succession ofspontaneous chemical reactions that produce increasingly complex chemical struc-tures. In the first edition of his book (1924) he suggested that such chemicalevolution would take place within an oxidizing atmosphere of the primitive Earth(it was the generally accepted view at that time that the early Earth had an oxidizingatmosphere). In the second edition (1938) he changed the early atmosphere to ahighly reducing environment. Similar ideas were simultaneously developed by theEnglish biologist John Haldane, who was the first to mention the concept of a“prebiotic soup” where chemical evolution took place, a term that became quitepopular in the scientific community studying the origins of life.Some paragraphs of Oparin’s book Origin of Life from 1924 show its actuality:

At first we found carbon scattered in the form of separate atoms, inthe red hot stellar atmospheres. We then found it as a componentof hydrocarbons which appeared on the surface of the Earth. …Inthe waters of the primitive ocean these substance formed morecomplex compounds. Proteins and similar substance appeared.…[They]…acquired a more and more complex and improvedstructure and were finally transformed into primary living beings –the forbears of all life on Earth.

He concluded quite optimistically, bearing promises of spectacular breakthroughsin the field within a few years:

We have every reason to believe that sooner or later we shall be ablepractically to demonstrate that life is nothing else but a specialform of existence of matter. The successes scored recently by Sovietbiology hold out the promise that the artificial creation of thesimplest living beings is not only possible, but that it will beachieved in the not too distant future.

Facing the hard reality of facts, he did temper his optimism and wrote as aconclusion of the second edition of his book in 1934:


We are faced with a colossal problem of investigating each separatestage of the evolutionary process as it was sketched here. …The roadahead of us is hard and long but without doubt it leads to theultimate knowledge of the nature of life. The artificial building orsynthesis of living things is a very remote, but not an unattainablegoal along this road.

As elegant as Oparin and Haldane’s ideas appeared to be, they were expressed at atheoretical level only. The experimental confirmation of the theory of chemicalevolution was provided in 1953 by Stanley Miller, a graduate student in thelaboratory of the Nobel Prize laureate Harold Clayton Urey. They conceivedand built an experiment to simulate a putative primitive Earth environment(Fig. 3.8).In this experiment a gaseous mixture of hydrogen (H2), methane (CH4), ammo-

nia (NH3), and water (H2O) was exposed to an electric discharge that simulated thatof storm lightning. The mixture was connected to a bulb filled with liquid waterthat could be heated. This experiment resulted in the production of a large amountof organic molecules, including several amino acids. Those measurements wereexperimental proof of the theory of chemical evolution. They showed that thechemistry between simple molecules, which were abundant in the atmosphere of


Fig. 3.8 Miller–Urey experiment, which simulates in the labora-tory the coupled chemistry between the primitive Earth atmos-phere (upper right bulb) and warm oceans (lower left bulb). Inthe first version, an atmosphere made of CH4, NH3, H2O, and H2

was considered. A spark discharge simulated storm lightning.

the primitive Earth, led to the synthesis of key compounds that in turn might haveled to the forms of life as we know it on Earth.The choice of a reducing atmosphere with C as CH4 and N as NH3 (Table 3.3)

was motivated by the following considerations:• CH4, NH3, H2O, and H2 had been detected in the atmosphere

of giant planets since the 1930 s.• All the primitive atmospheres of planets were identical, cap-

tured from the Solar Nebula.• Giant planets, cold and distant from the Sun, have kept their

original composition.

Therefore, Urey and Miller concluded that the current composition of the atmos-phere of giant planets of the Solar System was a good proxy for the composition ofthe atmosphere of the primitive Earth.

Table 3.3 Classification of planetary atmospheres, in terms oftheir redox potential, as a function of their composition.

Redox state of the atmosphere Composition

Reducing CH4, NH3, H2O, H2

CO2, N2, H2O, H2

CO2, H2, H2ONeutral CO2/CO, N2, H2OOxidizing CO2/CO, N2, H2O, O2

However, several recent findings disprove this argumentation. First, it is now quitewell established that telluric planets do not have sufficient mass to capture theSolar Nebula gas like the giant planets did. To do this, a minimummass of 10 to 15Earth masses is required. Only then can a forming planet efficiently trap thevolatile elements of the nebula to form its atmosphere. In addition, recent obser-vations have supported the conception that at a distance of one astronomical unit(AU) from the Sun – that is where the Earth accreted – the gaseous component ofthe Solar Nebula was probably dominated by CO2 and N2. Second, Earth, likeVenus and Mars, has a secondary atmosphere built from volatile compounds thatoutgassed from the mantle on one hand or were imported via meteorites andcomets on the other hand. Third, the composition of the primitive Earth atmos-phere was most probably dominated by CO2 and N2, in which organic syntheses arenot as efficient as in a reducing atmosphere (see Section 3.3).Even if the Miller–Urey experiment is not as conclusive as thought at first glance,

it was a great achievement because it showed that important prebiotic compoundscan be abiotically synthesized in environments simulating “natural” conditions. InSection 3.3 different kinds of such “natural” environments are presented that allowan interesting “prebiotic” chemistry.



Table3.4

Organ

icmolecules

synthesizedin

Miller-typeexpe

rimen

tsas

afunction

ofthecompo

sition

ofthestarting

mixture,

afterelectron

impa

ctor

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Photolysis

CH

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dunsaturated)

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RCO

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2CO,o

ther

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minoacidsan

dnitrogenated

heterocyclesafterhydrolysis

RH

(mostlysaturated)

HCN

RCN

(saturated)

ifN/C

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2ifN/C

>1H

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ther

aldehydes

Keton

esan

dalcohols

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minoacidsafterhydrolysis

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,Triton

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(saturatedan

dunsaturated)

HCN

andother

nitriles(saturatedan

dunsaturated)

includingHC3N

andC2N

2

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aldehydes

Keton

esan

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(saturated&unsaturated)

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O&other

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withlow

yields

Solid:C

arbo

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CO

+NH

3+H

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xygenated

organic

compo

unds

Solid:A


HCN,o

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CO

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RH

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CO

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Ven

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from

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=hydrocarbon

s

3.3Sources of Prebiotic Organic Molecules

3.3.1Endogenous Sources of Organic Molecules

3.3.1.1 Atmospheric SynthesesMiller and Urey thought that the first building blocks of life were synthesized inEarth’s primitive atmosphere. For the reasons discussed above, the gaseous mix-ture they chose is no longer considered to be representative of Earth’s earlyatmosphere. Table 3.4 shows some results obtained in different “Miller-type”experiments, using different gaseous mixtures and energy sources.Energy inputs through electric discharges represent lightning or electron inputs

in the atmosphere. For example, in the case of Saturn’s moon Titan, electronstrapped in the magnetosphere of Saturn cascade down into Titan’s atmosphere(see Chapter 9). Photolysis experiments simulate the energetic inputs of the Sunvia energetic UV photons that initiate chemical reactions. Using different energysources but the same atmosphere led to minor differences in the resulting prod-ucts.In contrast, a high sensitivity of the resulting syntheses to the starting gaseous

mixture was observed. Reducing gaseous mixtures, such as the one chosen byMiller and Urey, are the most efficient ones in the formation of complex organicstructures. However, current models of the primitive atmosphere of Earth suggesta rather neutral atmosphere, and such environments are not as efficient in initiat-ing chemical evolution as reducing ones. Figure 3.9 shows the yield in amino acids(percentage of initial C) as a function of the composition of the simulated atmos-phere when performing Miller-type experiments. In a reducing atmosphere, ifcarbon is in a reduced state (in the form of CH4), a large diversity of amino acids issynthesized in a rather efficient way. On the other hand, if carbon is in an oxidized

3.3 Sources of Prebiotic Organic Molecules 69

Fig. 3.9 Amino acid yield (percentage of initialC) as a function of the simulated atmospherecomposition in Miller-type experiments,performed at room temperature and in thepresence of liquid water. Results were obtainedafter 2 days of electric discharge experiments.

Partial pressure of N2, CO, or CO2 was 100 Torr(131 hPa). (A) A great diversity of amino acidswas produced. (B, C) Glycine predominated;little else was produced except a small amountof alanine (adapted from Miller and Lazcano2002).

state (CO or CO2), the amino acid glycine predominates, and the reaction yields aremuch lower than those using CH4. Moreover, in the absence of CH4, the yield ofamino acids drops significantly if the atmosphere is depleted in H2 and becomesmore and more neutral.Therefore, if the Earth mantle was less oxidized 3.8 billion years ago than today,

an important amount of CH4 could have been emitted through volcanism. In thiscase, endogenous Miller-type syntheses are possible. It has been estimated thatdepending on the redox state of the atmosphere, the endogenous production couldvary by several orders of magnitude, leading to a steady-state concentration oforganics in primitive oceans ranging from 0.4 10–3 g L–1 to 0.4 g L–1. However, itmust be stressed that to date the actual amount of reduced gas in Earth’s primitiveatmosphere is not known.

3.3.1.2 Hydrothermal VentsThe synthesis of organic compounds at the bottom of the ocean in hydrothermalvents (also known as black smokers; Fig. 3.10) has to be considered as anotherendogenous source of prebiotic molecules. Where oceanic plates drift apart, sea-water circulating through the ocean crust is heated up, and it dissolves andexchanges chemicals with the rock. At some places it springs back to the oceanfrom black smokers at a high temperature, enriched in gas, ions, and minerals.Catalytic clays and minerals interact with the aqueous reducing environment richin H2, H2S, CO, CO2, and CH4 (and possibly HCN and NH3). When exhaustedfrom the vent, the dramatic drop in temperature, from 350�C to about 2 �C, favorschemical reactions and polymerizations.It has been shown experimentally that amino acids can be synthesized in such

conditions (high temperature and pressure, reduced environment, and rich inminerals, which can act as catalyst). But one has to take into account that moleculessynthesized in the vicinity of black smokers can also be destroyed because of thehigh temperature. Nowadays, a volume equivalent to the world’s entire ocean


Fig. 3.10 Hydrothermal vents (photograph on the left courtesyof NOAA).

system circulates through hydrothermal vents every 10 million years. Their pres-ence would have fixed an upper limit on the concentration of organics in theprimitive ocean. More experimental data and field measurements are required toassess the feasibility of this mechanism.

3.3.2Exogenous Delivery of Organic Molecules

Remote sensing observations have given evidence that organic chemistry is veryactive in interstellar molecular clouds, as much in the gaseous phase as in the solidphase (interstellar ices) (see Chapter 2). HCN, HC3N, and HCHO have beendetected. Such molecules are of great astrobiological interest, as will be discussedin Section 3.4. Our Solar System is thought to be the result of the collapse of such acloud.Laboratory experiments simulating the conditions in the molecular clouds

predict the existence of molecules that are much more complex than the onesalready detected by remote sensing. These experiments aim to reproduce thechemistry occurring in interstellar ices. For this, gaseous mixtures consisting ofsimple volatile compounds (H2O, CO, CO2, CH4, NH3, CH3OH, H2CO, andothers), which have been detected in interstellar environments, are introducedinto a cryostat. These molecules then condense onto a cold finger where they forman icy mixture. If exposed to irradiations (either photons or charged particles) or tothermal cycles, chemical reactions between these simple compounds, which the iceis made of, lead to the formation of much more elaborated organic structures,which remain solid at room temperature. This refractory residue was called “yellowstuff” by Mayo Greenberg, the astrophysicist who conceived these laboratoryexperiments in the late 1970 s. From those simulations, one can infer that inmolecular clouds a large amount of organic matter should be frozen on condensa-tion nuclei made of silicates (Fig. 3.11).

3.3.2.1 CometsIt is generally accepted that during the formation of our Solar System the originalcomposition of interstellar grains was lost, because they were either incorporatedin the Sun or planets or pyrolyzed in locations close to the Sun. Turbulent radial


Fig. 3.11 Interstellar grain model: silicate core embedded ina mixture of complex refractory molecules, coated with ice ofvolatile compounds.

mixing in the Solar Nebula can bring interstellar ices to the warmest parts of thenebula where they would sublimate (Fig. 3.12). Inside the turbulent region, radialmixing brings interstellar grains close to the Sun, resulting in a loss of their initialcomposition. According to models, this turbulent region of the Solar Nebula mighthave extended up to the orbit of Neptune (about 30 AU). Beyond this region, grainsmight have remained in a cold environment and thus might have kept an unalteredinterstellar composition. Hence, the extension of the turbulent region determinesthe chances of keeping pristine interstellar matter in small, undifferentiated icybodies: the comets.Cometary models consider that interstellar organic matter undergoes different

levels of transformation before it will be stored in comets. In some models, cometsare considered to be aggregates composed of unaltered interstellar grains. From arather different point of view, comets are considered to be made of mattercompletely reprocessed in the Solar Nebula. Other models consider an intermedi-ate scenario, which is probably the more realistic one.Putting aside the discussion about the origin of cometary matter, observations

show an undeniable abundance of a large variety of organic compounds in comets.Molecules such as HCN, HCHO, or HC3N, which have been detected in severalcomets, might have an origin in the interstellar medium or might have been


Fig. 3.12 Scheme of the evolution of matter in our SolarSystem: from a natal molecular cloud, the Solar Nebula, untilits incorporation into Solar System bodies (Molecular cloudbackground courtesy of NASA, Solar System background cour-tesy of ESA).

produced inside the Solar Nebula. In either case, they are of the same astro-biological interest.In 1961, John Oro calculated the amount of organic molecules that could have

been delivered to the Earth via comets as follows: if one considers a typicalcometary nucleus with a density of 1 g cm–3, a comet 1 km in diameter wouldcontain about 2 � 1011 moles of HCN. This amount is equivalent to about 40 nmo-les cm–2 of HCN distributed over Earth’s surface. It corresponds to an amountcomparable to the yearly production of HCN by electric discharge in a CH4-richreducing atmosphere.As predicted in laboratory simulation experiments, in situ measurements in

close vicinity to the comets 1P/Halley (in 1986) and 81P/Wild 2 (in 2004) bearwitness to the existence of more-complex structures that – because of their highmolecular mass – remain in the solid phase on dust grains when ejected from thecometary nucleus. It must be stressed that the lack of liquid water in comet nucleiover long periods of time excludes the possibility of the existence of life in or oncomets – even if short periods of ice melting occur after nucleus formation causedby the decay of radioactive elements.Summing up, comets are considered to be exogenous sources of prebiotic

molecules of great astrobiological potential. This has been inferred from measure-ments in space as well as from laboratory simulation experiments. Therefore,comets are the target of several past, current, and future space missions, such asNASA’s Stardust (http://stardust.jpl.nasa.gov/) and Deep Impact missions (http://deepimpact.jpl.nasa.gov/) and ESA’s Rosetta mission (http://rosetta.esa.int/).

3.3.2.2 MeteoritesBy definition, meteorites are celestial bodies that reach the surface of the Earth.Meteorites – more specifically, those belonging to the carbonaceous chondritefamily (the most famous among them are the Murchison, Murray, and Orgueil)– are another exogenous source of organic molecules. Unlike comets, for which nodirect analysis of the nucleus composition has ever been made, a large number ofmeteorites have been studied with the most sensitive laboratory instruments.The current flux of meteorites is estimated to be about 10 tons per year and was

probably higher on the primitive Earth. A great number of organic molecules havebeen detected in meteorites, such as hydrocarbons; alcohols; carboxylic acids;amines; amides; heterocycles including uracil, adenine, and guanine; and morethan 70 amino acids in the Murchison meteorite. Recently, diamino acids havebeen found in the same object. This shows that molecules once synthesized inspace are able to survive a meteorite impact.Enantiomeric excess at the level of a few percent has been measured for some

amino acids in the Murchison and Murray meteorites. This could give us a key tounderstanding the origin of homochirality in living organisms on Earth. Unlikecomets, the parent bodies of meteorites might have gone through periods withliquid water, which might have led to more advanced stages of chemical evolution.It is interesting to note that some organic compounds extracted from carbonaceous


chondrites would spontaneously organize to form vesicles. They can be consideredas a type of primitive membrane that might have been used by the very firstorganisms.No space mission is currently scheduled to analyze the composition of carbona-

ceous asteroids, which are probably the parent bodies of chondrites. However,projects to explore a carbonaceous asteroid could certainly be planned in the yearsto come, and this will provide important information about the evolutionary stageof those bodies and the origin of their organic components.

3.3.2.3 MicrometeoritesMicrometeorites are another vector for exogenous delivery of organic molecules.With an asteroidal or cometary origin, their current flux is estimated to be about20 000 tons per year. They slowly sediment in the terrestrial atmosphere and thusundergo little warming that could destroy their organic content. Amino acids havebeen detected inmicrometeorites collected in Antarctica. Therefore, they could alsohave played an important role in the origin-of-life process.

3.3.3Relative Contribution of the Different Sources

The three different types of exogenous delivery of organic matter to the early Earth,i.e., by comets, meteorites, or micrometeorites, occurred not only on the Earth butalso throughout the Solar System. However, in order to reach an increased level ofcomplexity that could have led to life, those ingredients require liquid water.Unlike endogenous sources of organics, as inferred by Miller-type experiments

and the hypothesis of black smoker syntheses, which are still at an experimentaland conceptual level, exogenous deliveries are actually observed even nowadays.The contribution of the atmosphere as an endogenous source of organics is stillmodel dependent, and the contribution of hydrothermal vents to produce anddestroy organics lacks experimental data, whereas the exogenous delivery oforganics is an ongoing process.A clear distinction of the relative contribution of each source cannot be estab-

lished and seems to be out of reach as long as no other life forms are detected onanother planet that would be deprived of one or two of these factors. Only thencould it be said that one source is not essential. On the other hand, non-detection oflife on a planet with liquid water and at least one of the three factors could lead tothe conclusion that one specific source of organics is not sufficient for the origin oflife. But from an Earthling point of view, we can say that too many cooks can’t spoilthe prebiotic soup and that the processes leading from the rather simple buildingblocks of life discussed in this section to more elaborated structures are moreinteresting.


3.4From Simple to Slightly More Complex Compounds

In this section, the chemical pathways to synthesize the building blocks of life in atest tube are described. Some of themechanisms presented here are already familiarto students of chemistry or biology, although they generally are not presented froman astrobiological perspective. Students in other fields should not be afraid of thereactions presented here and should retain that simple mechanisms explain theproduction of most of the molecules considered essential to life.

3.4.1Synthesis of Amino Acids

The synthesis of amino acids has been known since 1850 and was discovered byAdolf Strecker. The mechanism is now well established (Fig. 3.13) and proceeds inliquid water as follows:

• In the first step, the addition of ammonia to aldehyde pro-duces an imine.

• In the second step, the addition of HCN onto the imineproduces an Æ-aminonitrile.

• In the final step, the hydrolysis of the -CN function (nitrile)into -CO2H (carboxylic acid) leads to the production of anamino acid.

In works published after the release of his first results in 1953, Stanley Millershowed that the production of amino acids during his experiments followed the

3.4 From Simple to Slightly More Complex Compounds 75

Fig. 3.13 Synthesis of an amino acid through Strecker synthesis,with H2CO, NH3, and HCN.

same synthesis processes (see Fig. 3.13). Other pathways are also possible, becauseit has been shown that an acid hydrolysis of HCN polymers results in theproduction of various amino acids.

3.4.2Synthesis of Purine and Pyrimidine Bases

Synthesis of the purine base adenine follows a spectacular prebiotic synthesispathway that proceeds by oligomerization of HCN in aqueous solution underthe influence of photons of 350 nm. This process was discovered by James P.Ferris and Leslie Orgel in 1966 (Fig. 3.14). It proceeds as follows:

• In the first step, the addition of four HCN compounds resultsin the formation of diaminomaleonitrile (DAMN).

• In the second step, a first-photon-step rearrangement ofDAMN results in the formation of diaminofumaronitrile andthen a second one in the formation of aminoimidazole car-bonitrile.

• In the last step, the addition of a fifth HCN molecule leads tothe production of adenine.

It is quite stunning to imagine that one of the most poisonous organic compounds,HCN, reacting with itself may result in the formation of one of the “letters” of thegenetic code, i.e., adenine, which is essential for life. Such are the ways ofchemistry.


Fig. 3.14 Synthesis of adenine from HCN.


Fig. 3.15 Synthesis of adenine and guanine from HCN and NH3.

Other pathways leading to the synthesis of purine bases are now known, such asthe ones presented in Fig. 3.15. In this example, a mixture of HCN and NH3 leadsto the production of adenine and guanine.Prebiotic pathways leading to the formation of pyrimidine bases have also been

investigated, such as the ones presented in Fig. 3.16. It is interesting to note thatcyanoacetylene (HC3N), the main reactant of the synthesis, is a compound detectedin the interstellar medium and comets and is also efficiently produced by the actionof spark discharges in CH4/N2 mixtures.The direct reaction of HC3N with cyanate (NCO–) gives quite low yields of

pyrimidine products, or it requires a quite large concentration of cyanate(>0.1 M) for higher yields. In 1995, Robertson and Miller showed that afterhydrolysis and formation of cyanoacetaldehyde, the reaction with urea in anevaporating solution (simulating primitive drying lagoons on Earth) forms anoticeable amount of cytosine.These are only a few illustrations of reactions that lead to the production of

purine and pyrimidine bases in prebiotic conditions. It is quite reasonable tobelieve that not all the pathways have been discovered yet, but the synthesis ofthese important compounds is not yet considered a problem for the chemistsstudying the origin of life.

3.4.3Synthesis of Sugars

Synthesis of the sugars required for the backbone of RNA and DNA molecules ismore difficult than that of the previously discussed compounds. Actually, it is notcomplicated to abiotically produce sugars. Butlerov found a simple way to obtainsugars as early as in 1861. This reaction is now known as the “formose reaction”


Fig. 3.16 Synthesis of cytosine and uracil from cyanoacetylene(HC2CN) and cyanate (NCO–).

(Fig. 3.17). It requires a concentrated formaldehyde solution and a suitablecatalyst, such as calcium hydroxide Ca(OH)2, calcium carbonate CaCO3, or clayminerals.The formose reaction results in a mixture of many kinds of sugars (more than 40

species), in which ribose is present at only a very low level. Hence, the formosereaction, although highly efficient, leads to an unspecific production of sugars.


Fig. 3.17 Synthesis of sugars through the formose reactionfrom H2CO.

Fig. 3.18 Structure of PNA, a hypothetical information-bearingmolecule based on peptides, and of RNA.

This makes it less interesting from an astrobiological point of view. Moreover, theformose reaction needs a concentrated solution of formaldehyde, which is not veryrelevant for the conditions of the primitive Earth. However, with the use of a propercatalyst, e.g., the clay mineral kaolin, sugars including ribose can be obtained fromlower concentrations (0.01 M) of formaldehyde.Therefore, in the frame of the RNA world hypothesis (see Chapter 4), the

question of why ribose among other sugars has been selected remains open.Because it is so complicated to find a suitable pathway for the prebiotic selectivesynthesis of ribose and to understand how ribose was selected among other sugars,alternative solutions have been suggested, such as a pre-RNA world. This could bebased, for example, on peptide analogues of nucleic acids, which are called “peptidenucleic acids” (PNAs) (Fig. 3.18), in which the sugar would be replaced by aminoacids. In this scenario, ribose would be incorporated into the structure of life’sinformational molecule at a later stage.

3.4.4Synthesis of Polymers

It has been shown in the previous sections that chemistry is not without solutionsto explain how the building constituents of life could have been synthesizedabiotically. The next step would be to associate the prebiotic elements into complexbiochemical material such as polypeptides (proteins) and polynucleotides (RNAand DNA). Here, prebiotic chemistry faces a further challenge.The linkage of amino acids to peptides is not favored from an energetic point of

view. The free enthalpy for the association of alanine (Ala) with glycine (Gly) is˜G� = 4.13 kcal mol–1. This means that the equilibrium is displaced to left and thedissociation of the di-peptide:

H-Ala-OH + H-Gly-OH H-Ala-Gly-OH + H2O (3.1)

˜G� = 4.13 kcal mol–1

37 �C, pH = 7

Reaction 3.1 shows that peptide bond formation is energetically not favored. Thereaction occurs in water and the equilibrium tends to be displaced to the left,because a water molecule is released during peptide bond formation.A thought experiment might illustrate this point. If one considers starting

peptide bond formation from a molar solution (1 mol L–1) of 20 natural aminoacids, thermodynamics says that a resulting protein of about 100 monomer unitswould have a concentration equal to 10–99 mol L–1. This means that 50 times thevolume of the Earth is required to get at least one protein!Other promising ways of polypeptide formation include catalytic synthesis on

mineral surfaces or evaporation–hydration cycle processes with activated aminoacids, e.g., with compounds, in which the acid function of the amino acid is

>


replaced by an ester function. However, these pathways are still under investiga-tion.The abiotic production of polynucleotides is even more complicated than that of

polypeptides. The reaction of a purine base with ribose in the solid state at 100 �Cresults in their association into a nucleoside with a yield of about 3%. But in thiscase, the base is not linked to the sugar at its “natural” place (Fig. 3.6). Moreover,nucleoside synthesis with a pyrimidine base has not yet been accomplished.As the next step, the reaction of the nucleoside with a phosphate needs to be

considered. Phosphorus is present in igneous rocks as fluorapatite (Ca5(PO4)3F)and in meteorites as chlorapatite (Ca5(PO4)3Cl). Heating at temperatures above100�C leads to the association of the compounds into a nucleotide, but, again, thelinkage of the phosphate does not occur specifically at the “natural” place. To date,the polymerization of nucleotides from their building blocks has not been achievedunder prebiotic conditions.

3.5Conclusions

In this chapter, the basic building blocks of life on Earth and simple ways tosynthesize them under prebiotic conditions have been discussed. But, having theblocks of life does not give a living system. Jacques Reisse, a Belgian chemistworking on the origin of life, says that at the present stage trying to understand thechemistry of the origin of life is like considering building a cathedral (life) buthaving only a pile of bricks (amino acids, sugars, purine and pyrimidine bases).Getting from the bricks to the cathedral, without a plan, an architect, or anyworkers (for the stones have to spontaneously combine themselves), is the chal-lenge chemists are facing. Even if the road is tricky, many chemists have decided todevote their studies to that complicated task. Year after year new discoveries aremade, but it is difficult to know how long it will take before, somewhere in alaboratory, an organic molecule synthesized under prebiotic conditions will behavelike a “robot,” spontaneously making copies of itself and capable of evolution. Todate, it is not even possible to say if such an achievement will ever be made. Whatdoes it take to turn chemistry into biology? Many tracks have to be investigated, andcrucial breakthroughs may not come from the laboratory studies but rather fromthe observation of other bodies in our Solar System. For example, how far does thechemistry go on Mars, Saturn’s moon Titan, or the Jovian moon Europa? Whatdoes it tell us about the origin of life on Earth? These are a few of the manyfascinating questions that need to be addressed in future studies.

3.5 Conclusions 81

3.6Further Reading

3.6.1Books or Articles in Books

Cronin, J., Reisse, J. Chirality and the origin ofhomochirality, in: M. Gargaud, B. Barbier,H. Martin, J. Reisse (Eds.) Lectures in Astro-biology, Vol. 1, pp. 473–515, Springer, Berlin,Heidelberg, New York, 2005.

Despois, D., Cottin, H. Comets: Potentialsources of prebiotic molecules for the earlyEarth. In: M. Gargaud, B. Barbier, H. Mar-tin, J. Reisse (Eds.) Lectures in Astrobiology,Vol. 1, pp. 289–352, Springer, Berlin, Hei-delberg, New York, 2005.

Greenberg, J. M. What are comets made of?A model based on interstellar dust, in: L. L.Wilkening (Ed.) Comets, pp. 131–163, Uni-versity of Arizona Press, 1982.

Maturana, H., Varela, F. J. Autopoiesis andCognition: The Realization of the Living,Reidel, Boston, 1980.

Miller, S., Lazcano, A. Formation of the build-ing blocks of life, in J. W. Schopf (Ed.) Life’sOrigin, pp. 78–112, University of CaliforniaPress, 2002.

Oparin, A. I. The Origin of Life, Foreignlanguages publishing house, 1924.

Oparin, A. I. Origin of Life, Dover publication,1938.

Oro, J., Cosmovici, C. B. Comets and life on theprimitive Earth, in: C. B. Cosmovici, S. Bow-yer, D. Werthimer (Eds.) Astronomical andBiochemical Origins and the Search for Life inthe Universe, Proceedings of the 5th Interna-tional Conference on Bioastronomy pp. 97–120,Editrice Compositori, Bologna, 1997.

Raulin, F. Chimie pr�biotique: exp�riences desimulation en laboratoire et “v�rit� terrain,”in: M. Gargaud, D. Despois, J.-P. Parisot(Eds.) L’environnement de la Terre Primitive,pp. 343–360, Presses Universitaires de Bor-deaux, 2001.

Raulin, F., Coll, P., Navarro-Gonzalez, R. Pre-biotic Chemistry: Laboratory Experimentsand Planetary Observations, in: M. Gargaud,B. Barbier, H.Martin, J. Reisse (Eds.) Lecturesin Astrobiology, Vol. 1, pp. 449–471, Springer,Berlin, Heidelberg, New York, 2005.

Schopf, J.W. Life’s Origin, the Beginnings ofBiological Evolution, University of CaliforniaPress, 2002.



Botta, O., Bada, J. L. Extraterrestrial organiccompounds in meteorites. Surveys in Geo-physics 2002, 23, 411–467.

Cottin, H., Gazeau, M. C., Raulin, F. Cometaryorganic chemistry: a review from observa-tions, numerical and experimental simula-tions. Planet. Space Sci. 1999, 47, 1141–1162.

Ferris, J. P., Hagan j., W. J. HCN and chemicalevolution: The possible role of cyano com-pounds in prebiotic synthesis. Tetrahedron1984, 40, 1093–1120.

Hennet, R. J.-C., Holm, N. G., Engel, M.H.Abiotic synthesis of amino acids under hy-drothermal conditions and the origin of life:

a perpetual phenomenon. Naturwissen-schaften 1992, 79, 361–365.

Miller, S. L. The production of amino acidsunder possible primitive Earth conditions,Science 1953, 117, 528–529.

Pascal, R., Boiteau, L., Commeyras, A. Fromthe prebiotic synthesis of �-amino acids to-wards a primitive translation apparatus forthe synthesis of peptides, Top. Curr. Chem.2005, 259, 69–122.

Shapiro, R. Prebiotic ribose synthesis: a criticalanalysis. Orig. Life Evol. Biosphere 1988, 18,71–85.


3.7.1Basic-level Questions

Question 3.1Describe the Miller–Urey experiment. What did we learn from its results? What

are its limitations?Question 3.2What are the main sources of organic compounds that are currently considered

for understanding the first steps of chemical evolution towards the origin of life?Could they be the same on Jupiter’s moon Europa? Why or why not?

3.7.2Advanced-level Questions

Question 3.3Draw a scheme describing an experiment attempting to simulate the chemistry

of interstellar ices.Question 3.4Describe the history of a C atom, from its synthesis in a star to its incorporation

into a living system on an imaginary planet harboring life.Question 3.5Describe the extent to which RNAmolecules could be considered living systems.


4From Molecular Evolution to Cellular LifeKirsi Lehto

In this chapter, contemporary cellular life is analyzed in order tosee which components are the most ubiquitous and conserved inall life forms and therefore assumed to be the most original func-tional units of life. Molecular analysis of these structures givessuggestions of how they were involved in early molecular evolutionand what functions they may have provided to the early (pre-cellular) replicators. By going backwards, step by step, one seeswhich inventions had to precede each stage of early evolution:genetically encoded proteins had to exist prior to the establishmentof the Last Universal Common Ancestor (LUCA), and RNA repli-cators, or replicating RNA analogues had to predate geneticallyencoded proteins. Special attention is given to the most conservedcomponents of the present life forms, considered to be relicts of theearly RNA world.

4.1History of Life at Its Beginnings

Our home planet was formed about 4.6 billion years ago. The initial conditions onthe young planet Earth were very harsh. The accretion process had heated theprotoplanet, and the temperature of the young planet was further increased by thegreenhouse phenomena caused by the dense atmosphere formed by H2O and CO2

and by continuing impacts from the colliding comets and meteorites. The initialplanet temperature was hot enough to keep the Earth’s crust in liquid form,forming a magma ocean on the surface. As the planet radiated heat, the temper-ature was reduced; when it came down to about 200 �C, with the prevailing highatmospheric pressure, the water vapor precipitated and rained down to formoceans. The dating obtained from the oldest zircon crystals indicates that liquidwater was present on the planet 4.4 billion years ago. The first Earth crust formed

4.1 History of Life at Its Beginnings 85


underneath the water. Because of heavy cometary and asteroid impacts, the con-ditions on Earth remained hot and violent for perhaps 500 million years; this timeis called the Hadean period.Conditions during the Hadean period are difficult to investigate because all the

rocks formed during that era have been thoroughly metamorphosed by the tectonicprocesses of the later times. The oldest still existing sedimentary rocks are locatedat Isua, Greenland, and date back to about 3.8 billion years. These rocks containsmall granules of sedimented carbon, which is specifically enriched in the 12Crather than the heavier 13C isotope. The enrichment of the lighter carbon isotope inthese sediments suggests that the carbon was once bound in biologically producedcompounds (see Chapters 1 and 2). The real biological origin of these carbondeposits has been questioned, but other nearly as old samples containing 12C-enriched carbon and fossilized microbial structures have been detected at two otherlocations: in the 3.5-billion-year-old sediments at Pilbara, western Australia, and atBarberton, South Africa. These findings suggest that life was well established, andapparently widely distributed on the Earth, at this very early stage – or soon afterthe heavy bombardment ended and the planet cooled to temperatures conducivefor life. It is not known at what temperature regimes life started. The mostthermotolerant contemporary life forms are known to propagate in temperaturesup to 113�C (see Chapter 5), but the prebiotic replicating macromolecules, and alsothe earliest cellular structures, may have been rather fragile and sensitive forhydrolytic conditions and most likely were not durable in very high temperatures.Since its early start, life has spread and diversified and now occupies all con-

ceivable ecological niches on the Earth (see Chapter 5). During its spread andaccumulation, life has also modified the environment and has profoundly changedthe conditions on planet Earth, including the chemical composition of the atmos-phere, the oceans, and the Earth’s crust. The long-term geological processes oftectonics, volcanism, weathering and erosion, as well as degrading processescaused by life itself, have completely reshaped and mixed multiple times theconditions that prevailed on the early Earth and have abolished most of thechemical and geochemical traces that were formed at this early time. Therefore,there are not any direct data of the conditions that once allowed or induced theorigin of life. It is even not know in what type of locations on Earth – or, potentially,on nearby planetary bodies – life did start. Thus, trying to trace back the veryearliest stages of this process becomes difficult and speculative.However, different scientific approaches may be used to try to resolve what kind

of conditions and what chemical compounds might have driven the life-producingreactions. Clearly, the origin of life has been a very complex process and needs to bestudied in many different fields of science. Astronomy is needed to resolve how theelements, the Solar System, and the planet Earth were formed in the first place.Geosciences are needed to resolve the conditions on the early Earth and thecomposition of the early atmosphere, the ocean, and the crust. Inorganic andorganic chemistry are needed to resolve how the elements, inorganic minerals, andvolatiles may have reacted to form small organic compounds and more complexorganics such as nucleotides and amino acids, which are the building blocks of life.

4 From Molecular Evolution to Cellular Life86

Further on, the quest is to resolve how these organic molecules may polymerizeand, in particular, how these reactions might conceivably have happened in pre-biotic conditions in the absence of genetically encoded enzymes and biochemicalreactions.Present-day life is solely driven by multiple protein-catalyzed (-mediated) bio-

chemical reactions and complex molecular interactions. The fields of biochemistryand bioinformatics study how these enzymes and other proteins now function andhow they have changed over the evolution of life. These studies can identify thegenetic sequences that are the most conserved (i.e., the oldest and most originalones) in different life forms. Of particular interest here are the reactions that stillare catalyzed not by proteins but by different RNA molecules. Such RNA enzymes(or ribozymes) may be derived from the very oldest life forms or from the erapredating the DNA-protein-based life forms.As a central part of the study of life, different fields of biology study the essential

structures and functions of life; how life reacts and adapts in its environment; andhow all functions are mediated, regulated, and coordinated on the cellular andmolecular level. All these integrated efforts are needed to construct an under-standing of what life is, how it has evolved through times, and, maybe, how itstarted in the first place.It may be assumed that the chemical and molecular evolution towards life

proceeded through a long cascade of different stages, initiated by spontaneousreactions between abundant chemical elements, or the chemical constituents oflife: carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphor (C, H, O, N, S, P). Insome high-energy conditions these elements formed reduced carbon and nitrogencompounds, such as hydrogen cyanide (HCN), ammonia (NH3), methane (CH4),and formaldehyde (HCHO). In suitable conditions these small organic molecules,together with water (H2O), reacted to form the building blocks of life: the nucleicacid bases (purines and pyrimidines), sugars and other hydrocarbons, and aminoacids (see Chapter 3 and Section 4.2). These, again via multiple chemical reactionsand interactions (which are not well understood as yet), formed polymers andmore-complex molecules. Some of the polymers gained the chemical potential tocopy themselves or to replicate, which was the first major transition towards theorigin of life. Replication initiated molecular evolution, which led to the inventionof genetically encoded proteins and, eventually, to the appearance of the firstcellular life forms. From then on, the diversification of life into all the species ofthe biosphere has been covered by Darwinian evolution.This chapter aims to trace back this process in order to visualize the different

stages of the progress from early organic molecules to cellular life forms. Instead ofstarting from the very beginning and progressing upwards, the chapter starts fromthe central features of cellular life as they are known now, because it is known forcertain that this is what eventually came out of early evolution (at the time ithappened, evolution was random and not directed – the outcome could be knownonly after it had happened). Then proceeding backwards, step by step, it discusseswhat types of simpler forms could have given rise to each of the new and morecomplex innovations.


4.2Life as It Is Known

4.2.1The Phylogenetic Tree of Life

Life is characterized by endless complexity. On the visible level one can observe themultitude of genera, species, forms, and individuals, each thriving in their owntypical ecological niches. Cells of higher organisms are differentiated into organsand tissues, which each present their specific form and function even that they allare regulated by the same genome of the same individual. Variation of species andsubspecies in the microbial world is vastly larger than that of the macrospecies. Themicrobial species can be separated into three different domains of life. Single-celledorganisms such as yeasts, ciliates, and flagellates, which do posses a nucleus in theircells, together with all the higher organisms belong in the domain of Eukarya. Thecells that do not posses a nucleus belong to the prokaryotes, which again belong totwo distinct domains, the Bacteria (or by older nomenclature, the Eubacteria) andthe Archaea (older name, the Archaebacteria). These three domains of life (Eukarya,Bacteria, andArchaea) each constitute their own and separate lineages of life and canbe distinguished from each other by multiple genetic and biochemical markers.The three domains of life share a large number of common features that are

ubiquitous to life, or are the same or very similar in all living organisms. It isbelieved that these features were inherited from a common ancestor of all lifeforms, the Last Universal Common Ancestor (LUCA). However, the properties ofLUCA at the time of diversification and the exact sequence of the separation of thethree lines are still unclear. Clearly, the common ancestor has developed through acascade of gradually increasing complexity, and it is not quite clear, which stagewas The Last Common One. As reviewed by Delaye and coworkers (2005), it mighthave been a community of simple precursors of life, the so-called progenotes (seeSection 4.3.2), or even a community of free-living replicating molecules, predatingthe establishment of cellular life. However, recent phylogenetic studies (i.e.,studies of the lineages and relatedness of known organisms through statisticalcomparison of their genetic sequences) by, e.g., the groups of Lazcano andDoolittle, indicate that LUCA was a well-established cell line. The properties ofLUCA will be discussed below.

4.2.2Life is Cellular, Happens in Liquid Water, and Is Based on Genetic Information

From unicellular microorganisms to all higher life forms, all life on Earth iscellular (Fig. 4.1). Prokaryotes are single-celled organisms. The cells are simpleand usually devoid of any internal membrane structures (except for the photo-synthetic cyanobacteria, which possess intensive photosynthetic membranes). Thecells are spherical, ellipsoid, elongated, or rod-shaped (see Chapter 5) and of sizesvarying from 0.1 �m to 600 �m, depending on the species.


All eukaryote cells have intensive internal structure. Cell organelles include• the nucleus (contains the chromosomes or the genomic

DNA);• mitochondria (energy-producing organelles);• the endoplasmic reticulum (internal membranes),• the Golgi apparatus (membranous vesicles for protein pro-

cessing and transport),• lysosomes and peroxisomes (for containment of degradative

enzymes and wastes); and• chloroplasts (photosynthetic organelles; in plant cells only).

The cells of all eukaryotes are very similar to each other, except that the plant cellshave thick and rigid cell walls and contain numerous chloroplasts (or other types ofplastids). Typical sizes vary from 10 �m to several hundred micrometers, but somelarge cell types occur (of a size up to more than 1 m for some nerve cells).Multicellular organismsmay be conceived as tightly bound colonies of individual

cells. The cells are entities contained within the cell membrane, which separates

4.2 Life as It Is Known 89

Fig. 4.1 All life is cellular. (A) Microscopic view of (unidentified)bacterial cells. (B) Scheme of a eukaryotic cell (animal cell on theleft, and plant cell, with a rigid cell wall, on the right) showing theintensive internal structure.

the cell from its environment but also allows sophisticated communication withthe environment. The communication includes the intake of water and necessarynutrients, excretion of waste products, receiving of chemical signals via differentreceptor molecules, and sending off signals via secretion of different molecules.Thus, the cells dynamically communicate with their environment. All communi-cation through the membrane is mediated via specific proteinaceous channels andstructures embedded in the membrane, because the membrane itself is a hydro-phobic barrier and therefore impermeable to water-soluble molecules.Inside the cells, life is a chemical process where multiple biochemical reactions

take place in aqueous solution. Water functions as the solvent and carrier for ionicand polar molecules, and also is a reacting component in many reactions. Wateralso serves as the exclusion medium to allow the lipid molecules to assemble andformmembranes, and as the medium that interacts with proteins, helping them tofold into their three-dimensional forms. Therefore, water provides a suitableenvironment for the different cellular reactions and for the assembly of importantcellular structures. It provides turgor (internal pressure) and strength to the cells.Water is such an essential environment and requirement for all the life functionsthat it seems likely that the origin of life had to happen in an aqueous environment(see Chapter 1).Proteins, or gene products, have a multitude of essential roles in the cells. They

form several different structures, such as the cytoskeletons in eukaryotes, com-ponents of cell walls, and the porous structures in cell membranes. They regulatereactions such as gene expression and genome replication, and they function insignal transduction by interacting with different target molecules. Still anotherarea where proteins are essential for life is in the (regulated) catalysis of all thereactions going on inside the cells. Most cellular molecules are both synthesizedand degraded via multi-step reaction pathways – and none of these reactionswould happen, at least at any desired rate, without the assistance of proteinaceousenzymes. Even the energy conversion and -releasing reactions have to be medi-ated via enzymatic catalysis so that they happen in a controlled and regulated


Fig. 4.2 Chemical reactionrates in dependence of sub-strate concentration, with andwithout enzyme catalysis. En-zymes speed up reaction ratesvery strongly as compared tonon-catalyzed reactions andmake them happen efficientlyeven at very low substrate con-centrations. The maximum rateof reaction is reached when theenzyme becomes saturatedwith the substrate molecules.

fashion. The enzymes themselves do not participate in the reactions but associatewith the reacting molecules and hold them in such a conformation that thereaction can proceed. Enzymatic catalysis is capable of raising reaction rates bymany orders of magnitude, from nearly zero to very high, and in practice mostbiological reactions would not happen in physiological conditions without enzymecatalysis (Fig. 4.2).Proteins form the tools and the structures in the cells, and genetic information,

encoded in the genomic deoxyribose nucleic acid (DNA), specifies how these toolsand structures are made. Life depends on the function of the proteins and thus onthe genetic information coding for them. Proteins are composed of long chains ofdifferent amino acids, and the sequence of the amino acids in these chains isdetermined by the genes coding for them. From the DNA, the protein-codingsequences are first copied into ribose nucleic acid (RNA) and from this areconverted into amino acid sequences in peptide chains. RNA is a polymer moleculevery similar to DNA; it is composed of similar nucleotide components, with onlythe small difference of an OH group, rather than H, being connected to the carbonin position 2 (2’) in the pentose sugar ring (thus, the sugar is ribose instead of


Fig. 4.3 Structure of the componentsof genetic material: the nucleic acidbases adenine, guanine, cytosine,thymine, and uracil; the deoxyriboseand ribose sugar molecules; and thephosphate moiety.

deoxyribose) (Fig. 4.3). However, this OH group is very reactive and, differing fromthe DNA, makes the RNA polymers very fragile, unstable, and short-lived.

4.2.2.1 Genetic InformationThe complexity of life extends strongly to the molecular level, i.e., to the nucleicacid and protein level inside the cells. The genetic information is encoded in thegenomic DNA in the sequence of four different deoxyribonucleotides (or, in short,nucleotides), which are the phosphorylated form of adenosine (A), guanosine (G),cytosine (C), and thymidine (T) nucleosides. In RNA, the uridine nucleoside isused instead of the thymidine nucleoside. The nucleosides themselves are formedof the corresponding bases (adenine, guanine, cytosine, thymine, and uracil); ofthese, A and G bases are purines and C, T, and U bases are pyrimidines (Fig. 4.3).The bases are covalently bound to a deoxyribose (in DNA) or ribose (in RNA) sugarto form nucleosides. These are phosphorylated at the carbon at their 5’ position toform nucleotides, and these again are connected into long chains via phospho-diester bonds between the 5’ and 3’ carbons (these are the carbons in positions 3and 5 in the ribose ring) of the adjacent sugars (Fig. 4.4).The number of nucleotides in the genomes varies largely between different

species. The genomes of the smallest prokaryotes are composed of about 0.5 � 106

nucleotides, while the genome of the bacterium Escherichia coli is composed of4.8 � 106 nucleotides. The smallest eukaryotic genomes are about an order ofmagnitude larger, but the more complex ones are many orders of magnitude largerthan the prokaryote genomes. The genome of wheat, for instance, is composed of


Fig. 4.4 Schemes of DNA. (A) The deoxyribonucleotide polymerformed by diester bonds between the 3’ and 5’ carbons ofadjacent nucleotides; (B) the double helix of two DNA strandsshowing the base pairing of the nucleic acid bases.

about 17 000 � 106 nucleotides, the human genome of 3 400 � 106 nucleotides, andthat of the fruit fly of 97 � 106 nucleotides (Table 4.1). Further, the number of genesvaries a lot, being about 400 in the smallest endosymbiotic bacteria (Buchneraaphidicola) and some hundreds of thousands in the largest genomes.

Table 4.1 Genome size and coding content of different types oforganisms.

Species Domain Genome size(million bp)[a]

No of genes Coding (%)

Mycoplasma genitalium Bacteria 0.58 470 100Escherichia coli Bacteria 4.8 4 288 100Methanococcus jannaschii Archaea 1.7 1 738 100Saccharomyces cerevisiae Eukarya 12 6 144 70Caenorhabditis elegans Eukarya 100 18 266 25Arabidopsis thaliana Eukarya 100 25 498 31Homo sapiens Eukarya 3 400 32 000 28[b]

1.4[c]

Triticum aestivum Eukarya 17 000 60 000 Not determinedAmoeba dubia Eukarya 670 000 Not determined

a Million base pairs = number of nucleotides.b Total.c For proteins.

The very large genomes, e.g., those of wheat or amoebas, have not been sequenced.Therefore, their accurate sizes and gene contents are not known as yet but can beestimated from their physical properties. It is clear that genome sizes are correlatedwith neither the size nor the complexity of the different species. This seemingparadox is explained by the fact that the large eukaryotic genomes contain largeamounts of non-coding DNA. In humans, for instance, only about 1.5% of thegenomic DNA codes for protein products, and only about 28% of it is transcribedinto RNA. A large part of the remaining DNA is composed of highly repetitivesequences, which are often referred to as “junk-DNA.” However, the non-codingDNA is not all insignificant, because some of those sequences have importantfunctions as structural elements of the DNA or have contributed (or may contributein the future) to the evolution of the genome.Although the cellular genomes are very large, they function in very controlled

manner. Among all the multiple genes, and in the middle of the very large non-coding sequences, the functional genes are expressed in a highly coordinatedfashion: the amount, timing, and location of the expression of each gene areaccurately regulated. The gene regulation is mediated mostly by different proteins– but in many cases also by small, non-coding RNAs.Different proteins, RNAs, membranes, and small soluble molecules such as

sugars and salts fill up the cellular contents, up to a level of molecular crowding in


the interior space. Although the cellular contents are very complex, their centralfunctions are uniform between all different cells and between all species. Partic-ularly, the genetic code itself and its expression mechanism are the same, inprinciple, in all species (Fig. 4.5).

4.2.2.2 The Genetic Code and Its ExpressionThe genetic information is encoded in the nucleotide sequences in groups ofthree adjacent nucleotides, the codons, each corresponding to specific aminoacids (or a stop sign). Although the four nucleotides (A, G, C, and T in DNA;in RNA, T is replaced by U) can be organized into a total of 43 = 64 different tripletcombinations, only 20 different amino acids are utilized and coded for in thecurrent life forms – although some prokaryotes use 22 different amino acids.Thus, the coding system includes some redundancy: several codons code for thesame amino acid (Table 4.2). Each gene is composed of a set of triplet codons. Thecode of each gene (or the open reading frame, ORF) starts at a specific ATG tripletin the DNA and continues until it reaches one of the following triplets: TAG,TAA, or TGA, which do not code for any amino acid. These stop codons mark theend of the gene (Table 4.2). In eukaryotes the genes are often interrupted byintervening sequences (introns) that must be removed from the sequence duringits expression process.


Fig. 4.5 Flow chart of the expression of genetic information.


Table4.2

Thegene

ticcode

,com

posedof

triplets

ofthefour

nucleicacid

basesuracil(U

),cytosine

(C),ad

enine(A),

andgu

anine(G

),an

dtheirinform

ation(aminoacid

orstartor

stop

codo

n).

Firstbase

Cod

onSecond

base

UInform

ation

Cod

onSecond

base

CInform

ation

Cod

onSecond

base

AInform

ation

Cod

onSecond

base

GInform

ation

Thirdbase

U U U U

UUU

UUC

UUA

UUG

Phen

ylalan

ine

Phen

ylalan

ine

Leucine

Leucine

UCU

UCC

UCA

UCG

Serine

Serine

Serine

Serine

UAU

UAC

UAA

UAG

Tyrosine

Tyrosine

Stopcodo

nStopcodo

n

UGU

UGC

UGA

UGG

Cysteine

Cysteine

Stopcodo

nTryptop

han

U C A G

C C C C

CUU

CUC

CUA

CUG

Leucine

Leucine

Leucine

Leucine

CCU

CCC

CCA

CCG

Prolin

eProlin

eProlin

eProlin

e

CAU

CAC

CAA

CAG

Histidine

Histidine

Glutamine

Glutamine

CGU

CGC

CGA

CGG

Arginine

Arginine

Arginine

Arginine

U C A G

A A A A

AUU

AUC

AUA

AUG

Isoleu

cine

Isoleu

cine

Isoleu

cine

Methionine,

startcodo

n

ACU

ACC

ACA

ACG

Threon

ine

Threon

ine

Threon

ine

Threon

ine

AAU

AAC

AAA

AAG

Asparagine

Asparagine

Lysine

Lysine

AGU

AGC

AGA

AGG

Serine

Serine

Serine

Serine

U C A G

G G G G

GUU

GUC

GUA

GUG

Valine

Valine

Valine

Valine

GCU

GCC

GCA

GCG

Alanine

Alanine

Alanine

Alanine

GAU

GAC

GAA

GAG

Asparticacid

Asparticacid

Glutamic

acid

Glutamic

acid

GGU

GGC

GGA

GGG

Glycine

Glycine

Glycine

Glycine

U C A G

The genetic code is interpreted (or expressed) in a multi-step process (Fig. 4.5) thatconverts the sequence of the nucleotide triplets into a linear sequence of thecorresponding amino acids (Table 4.2). First, the sequence of the target gene iscopied (transcribed) into a messenger RNA (mRNA). The mRNA contains thesame sequence as the corresponding DNA, but in contrast to DNA, the RNApolymer is short-lived and is used only for short-term expression of the code.The mRNA associates with the two subunits of the ribosome, which then movesalong the mRNA and recognizes the triplet code, starting from the first AUG codonon the mRNA (corresponds to the ATG on the DNA). The nucleotide triplets arerecognized by the anticodon triplets of the aminoacylated transfer RNAs (tRNAs),which enter into the ribosome complex and bring in the specific amino acidscorresponding to each triplet codon. The peptide bonds between the adjacentamino acids are formed by the catalytic RNA component of the ribosome (riboso-mal RNA, rRNA). As these amino acids are brought into the reaction complex, theribosome joins them into a long chain or “translates” the nucleotide sequence intoan amino acid sequence (Fig. 4.5). The produced amino acid chain is initially calleda polypeptide, but after it folds into the accurate three-dimensional structure, itbecomes a functional protein.Thus, the components needed for the expression of the genetic code are the

mRNA, the tRNAs and the amino acids, and the ribosomes. The ribosome itself iscomposed of multiple proteins and RNAs (varying from 52 to 79 proteins and fromthree to four RNAs in different species). Each of the steps of the gene expression(transcription, tRNA amino acylation, and the translation itself) requires multipleaccessory proteins for correct function and regulation. This strong protein depend-ency of the whole gene expression process creates a dilemma similar to the one ofthe chicken and egg. Proteins are required for expression of the genetic code as wellas for the maintenance (or replication) of the code, and the code is needed for theexpression of the proteins. Thus, how could the genetic DNA first be generated andreplicated, and how was its expression machinery first established – how did thiscyclic process get started?It is assumed that the storage and expression of the genetic information were the

first hallmarks for life as we know it and that these were the key elements in themolecular evolution that led to the birth of the LUCA. They existed already at thetime of the LUCA, and they required functions such as genome replication,transcription and translation, and pathways for amino acid and nucleotide syn-thesis. These functions are so essential for present life that their origin is thecentral part of the question of the origin of life as a whole.

4.3Last Universal Common Ancestor (LUCA)

The features that occur in all life forms are essential to life. Therefore, they shouldhave been present already in the earliest established cellular life, i.e., in the LUCA.Such conserved features include


• the enclosure or containment in cell membranes,• the genetic code, and• the translation machinery for the expression of the code

(the ribosomes, tRNAs, and amino acids).

Some enzymes related to RNA and amino acid biosynthesis and degradation and toenergy production and use (cell metabolism) also are common to all cellular life. Afurther curious detail that is fully conserved in all cellular life is the symmetrybreaking, or homochirality, occurring in its central molecules: all the amino acidsused in the cellular proteins are of the same stereoisomer type, which is the left-handed (L)-configuration (see Chapter 2), and the deoxyribose and ribose sugarsused in all the nucleotides are of the right-handed (D)-configuration only, meaningthat the bond between the carbons in positions 4 and 5 points up, not down(Fig. 4.4).

4.3.1Containment in a Cell Membrane

As mentioned earlier, all life on Earth is cellular, which means that it is allcontained within, and separated from its environment by cell membranes. Thiscontainment is important for many reasons. Themolecules synthesized in the cellsdo not escape into the environment, and the concentrations of the intracellularmolecules are maintained at desired levels by regulating their synthesis anddegradation. Molecules from outside are transported in and out in a regulatedmanner, and the cellular molecules interact and function in amutually coordinatedway. Further, because the cell membrane physically connects the genomes withtheir respective gene products, the selection for beneficial products and functionsbecomes targeted to their corresponding coding sequences, i.e., the genes canevolve based on their products. The physical connection also allows the jointmaintenance of different segments of the genomes and allows their coevolutiontowards synergistic functions. All in all, the cell membrane allows all cellularcomponents to function and evolve as one coordinated entity and unit.The excellent utility of present-day membranes is related to their highly

sophisticated properties. Cell membranes are formed of amphiphilic (i.e., oneend is hydrophobic and the other end is hydrophilic) molecules called lipids,which aggregate in water and assemble into bilayers (see Chapter 3). These lipidbilayers are themselves impermeable to water, but they are spanned by severaldifferent proteins that serve as transport channels for water-soluble moleculesand as receptors for external signals and cues. The cells may also adjust theproperties of their membranes by changing their protein components or bychanging the saturation level of lipids according to temperature. Cells continu-ously produce new lipids for the growth of their membranes, and different lipidsare produced to construct membranes for different compartments. Thus, mem-branes in current cells are very dynamic and functional. However, the situationwas quite different at the time prior to the existence of the proteins needed for

4.3 Last Universal Common Ancestor (LUCA) 97

lipid biosynthesis or for membrane transport channels. How could the cells becontained at this stage?It is possible that some type of membrane was formed in the early world by

spontaneous assembly of abiotically formed lipids. It has been shown that differentpolar hydrocarbon derivatives, containing 10 or more carbons in their hydrocarbonchain, are amphiphilic molecules that may assemble into bilayers, and these againmay spontaneously form vesicles in aqueous environments. Such aliphatic (or linear)and aromatic (or circular) hydrocarbons are present, for instance, in the carbonaceouschondrites (see Chapter 3). Hydrocarbon–lipid vesicles might have enclosed theearliest genomes and functioned as compartments for their replication. However,this scenario involves severe problems. Because the hydrophobic lipid membranesseparate the organism from the surroundings, they may prevent access to theirresources, such as useful molecules available in the surrounding. Further, becausethe organism is closed inside a “dead” membrane, it may not be able to expand ordivide or to allow its progeny to accumulate beyond its own original compartment.Several membrane chemists, e.g. the research groups of Deamer, Luisi, and

Szostak, have attempted to resolve the assembly and the functional parameters ofspontaneously assembled membrane vesicles. They have shown that the perme-ability of the bilayer membranes is related to the length of the aliphatic carbonchains: modified hydrocarbons of less than 14 carbons are permeable for smallionic molecules, such as amino acids and phosphates. Actually, lipid membranesformed of carbon chains of less than 10 carbons are too permeable to maintain anyion gradient. The membrane vesicles formed of longer fatty acids, such as oleicacid, are semipermeable: small molecules, such as nucleotides or amino acids, maydiffuse through them while large polymers may not. This property would allowspontaneous uptake of nucleotides into the vesicles and retention of the polymersinside them. This process would increase the osmotic potential inside of thevesicles and cause the growth of the membrane via incorporation of more fattyacids drawn from emptier vesicles or frommicelles. Thus, themere hydrophobicityof fatty acids or of other lipid molecules may have caused the prebiotic assemblyand function of primitive, cell-like structures. Indeed, assembly and growth, andeven division of such lipid vesicles, have been demonstrated in laboratory con-ditions. Likewise, nucleotide and amino acid polymerization inside the vesicle hasbeen induced, simulating the assembly of small, artificial cells.To have an adequate supply of the lipids (or of amphiphilic carbon chains) for

membrane assembly, the LUCA would have needed the pathways to synthesizecarbon chains containing at least 10 carbons. A significant dilemma related to theorigin of the lipid biosynthesis pathways is that in present life two completelydifferent types of lipids are used for cell membranes: the Archaea use isoprenoid-type carbon chains (polyunsaturated hydrocarbons with methyl side chains), andthe Bacteria and Eukarya use fatty acid–type (unbranched) carbon chains. Thesetypes of carbon chains are produced via completely different pathways, and thepathway utilized in Archaea does not even exist in Eukarya or in Bacteria. Thus, it isdifficult to deduce what kind of lipid biosynthesis might have been utilized in theLUCA and how this early membrane synthesis gave rise to two different mem-


brane compositions. It is possible either that several different lipid biosynthesispathways were established in the LUCA population, or that the cellular membranesynthesis pathways were established after the divergence of the three domains.However, this latter scenario would leave open the question of how, or in what, theLUCA was contained.It has been suggested by some geochemists that prebiotic reactions and early life

would have utilized some other types of compartments, formed of inorganic surfa-ces. W�chtersh�user (2003) has proposed that prebiotic chemistry might haveoccurred on surfaces of clays or minerals where the earliest cells might then haveassembled. These minerals would have catalyzed the reactions and stabilized theforming polymers (see Chapter 1). Martin and Russell (2002), Koonin and Martin(2005), and Brown propose that the porous, chimney-like structures of metal sulfide(mainly FeS) precipitates, formed at the hydrothermal vents at the bottom of theearly ocean, functioned as chemically rich, protective hatcheries that providedcontainment and suitable chemical conditions for the chemical evolution towardslife. The main attractions of these latter ideas are as follows.

• Firstly, those metal sulfide mounts were formed from amultitude of small, interconnected compartments, whichmight have served as containments for chemicals and ascatalytic surfaces for reactions.

• Secondly, the hydrothermal vents produced a continuousflow of warm geothermal fluid, full of several different re-duced chemicals, and it maintained a strong reduction gra-dient between the H+-rich geothermal fluid and (supposedly)alkaline seawater, driving the reduction chemistry of themolecules.

• Thirdly, the hydrothermal vents produced a temperaturegradient, providing convection flows to cycle the macromo-lecules between double-stranded and single stages (discussedin Section 4.6).

The combination of all these factors might have allowed the evolution of complexmolecular communities in the cell-like inorganic compartments, until they wereadequately competent to produce lipids and proteins for cellular membranes andstructures and might escape from the hatchery to self-sustained life in the outsideworld.

4.3.2Genes and Their Expression

One experimental way to study what properties and functions were present in theLUCA is to look at which genes or sequences are still common to all the organismswhose sequences are known today (assumably derived from the common origin).Lazcano and coworkers compared a set of fully sequenced genomes and found 283genes that are highly conserved in all Eukarya genomes, 24 that are highly


conserved in Bacteria, and 145 that are conserved in Archaea. In all domains thesegenes include putative ATPases (for conversion of proton gradients into adenosinetriphosphate [ATP] synthesis and for utilizing the energy of ATP), genes involvedin transcription and translation, as well as RNA helicase and enolase, phosphor-ibosyl pyrophosphate synthase, and thioredoxin genes, which are involved innucleotide biosynthesis and RNA degradation. Such genes, if they were presentin the LUCA, indicate that the organism possessed means for maintaining itsgenetic information (at least in RNA form) and a translation system. Because theATPases locate in the membranes and produce ATP (as energy compound) byutilizing proton gradients formed across the membranes, this indicates that LUCAhad a cell membrane and produced and used energy in the form of ATPmolecules.Another approach to model primitive life is to analyze what would be the

minimal set of genes required by the simplest cells today. Several groups ofbioinformatists have worked on such questions. Gill and coworkers have searchedthe genomes of the smallest existing cells (bacterial and archaeal species, whichlive as endoparasites inside their host cells) for the set of genes that seemmandatory for them all. The living environments of these species are chemicallyvery rich, and the cells may obtain a large part of all their required biochemicalprecursors from their hosts. Therefore, they have lost the corresponding genesfrom their own genomes and have evolved, by reduction, towards ultimately smallgenomes. Comparison of the genomes of such species revealed that they have 206genes in common. All species have additional genes that allow them to survive intheir specific environment (host), but these 206 genes seem to comprise theobligatory set of genetic information required in all these species. Thus, it canbe reasoned that a comparable set of genes is essential for any cellular life, evenwhen living in the most protected and nutrient-rich conditions. Thus, if the LUCAwas a well-established cellular species, sustained in its own (probably chemicallyrich, easy, and protected) environment, it probably had to possess at least thisnumber of gene different functions.As the early organisms evolved to more complex, the initial sequences were

converted via mutation and recombination to code for new functions. The genomesgrew larger by duplicating, recombining, and modifying what they already had:new genes were often produced from previously existing ones, by recombining andmodifying functional protein domains (3-dimensional structures). Recent proteinstructure analysis by Doolittle and coworkers has identified a set of 49 protein-folding domains (or folding super-families) that are present in all analyzed ge-nomes of the three domains of life, suggesting that these protein-folding structureswere already present in the LUCA. Again, these protein structures occur in theproteins related to translation and to metabolic and glycolytic enzymes.So far, it has been reasoned that LUCA was a fairly complex organism. But how

did it diversify into the three domains of life that we know today? The threedomains differ from each other in such ways that their direct descent from oneanother, in a fixed order, is difficult. Each pair of domains shares some featuresthat are lacking from the third domain (Fig. 4.6), so it seems that none of them isdirectly derived from the others.


Because the deviation of the three domains from the LUCA is difficult to traceback, the question of the order of the establishment of the three domains remainsopen, i.e.:

• whether the prokaryotes differentiated as two branches fromthe LUCA and then formed the eukaryotes later by mutualfusion;

• whether the eukaryotes were derived directly from the LUCAand later gave rise to the prokaryotes (e.g., by plasmid escapeand reduction processes); or

• whether the three domains diverged separately from a mixedLUCA population.

When this question has been addressed by phylogenetic studies, different resultshave been obtained from different genes. For instance, the classical phylogenetictree based on 16S-rRNA sequences, first produced by Woese and coworkers in1990, shows the early deviation of the Bacteria and Archaea domains, with thethermophilic Bacteria and Archaea at the base of the different branches, and thelater deviation of the Eukarya domain from the Archaea (Fig. 4.7A). However, someauthors, e.g., Poole and Forterre, suggest that the phylogenetic analysis may notaccurately resolve the most ancient sequences: after very long (or very fast)evolution, sequences may become so saturated with mutations that they appearas more conserved in the phylogenetic analysis.When different protein gene sequences are analyzed, diverse phylogenetic trees

are produced for the different sequences. This may indicate that the domains havenot evolved as separate lines but rather that the genes have been mixed by stronglateral gene transfer after the separation of the domains.It is now widely discussed (see reviews by Pennisi and Doolittle) that the

intensive lateral gene transfer between species, and even between domains, mayhave mixed the initial lineages so effectively that it may be difficult to trace back anyoriginal sets of genes associated with the early phylogenetic lines. Such lateral genetransfer would have been possible because the newly separated lineages were stillvery simple, similar, flexible (nonspecific), and rudimentary in their functions.Therefore, they might utilize the same novel functions and structures, even if those


Fig. 4.6 Distribution of some key conservedfeatures among the three domains of life: eachof them is shared by two domains only.

were transferred across the domain borders. The DNA exchange could have beenmediated via cell fusions or via direct DNA uptake (gene transfer or cellularconjugation) – or via third parties, such as viruses or plasmids (gene transductionor transformation).Particularly in eukaryotes, the uptake of foreign (prokaryotic) DNA may happen

via eating up (endocytosis) of foreign cells. This process is still a distinct function of


Fig. 4.7 Phylogenetic lineage of the three domains of lifedetermined by different genetic sequences. (A) 16S ribosomalRNA sequence (adapted from Woese et al. 1990); (B) severaldifferent sequences (adapted from Doolittle 1999).

some eukaryotic cells. Mitochondria and chloroplasts are well-known examples,indicating that endocytosis of other species has occurred in the history of differenteukaryotes. In these instances the engulfed prokaryotes were maintained intact inthe cytoplasm and established as beneficial endosymbionts, or organelles, of thecells. Considering the strong lateral gene transfer, the tree of life at its earlier stageslooks rather like a bush (Fig. 4.7B).

4.3.3Hypothetical Structure of the LUCA Genome

The dilemma of the differentiation of the three domains relates to the question of thetype and structure of the LUCA genome. It is commonly thought that LUCA shouldhave been similar to the simplest life forms existing today, the prokaryotes. Accord-ingly, it should have been driven by a small, circular DNA genome. However, Pooleand Forterre and their coworkers argue that the circular, supercoiled prokaryoticgenomes with a single origin of replicationmight represent a later adaptation to veryfast and efficient replication strategies.The most primitive DNA genomes may havebeen linear, like the RNA genomes (see Section 4.4), which are thought to havepreceded the DNA genomes. One argument supporting the idea that the eukaryote-like linear genome structure is themost original one is that specific catalytic RNAs –apparent relicts of the earlier RNA genomes – are still used to process different RNAproducts in the eukaryotes (Table 4.3), while many of them have been replaced bymore efficient (and advanced) protein catalysts in the prokaryotes. Likewise, tRNA-like components are still utilized in the enzymes (telomerases) that maintain thetermini (telomeres) of the linear eukaryote chromosomes, suggesting that theseterminal structures are derived from the genomes of RNA-based life.The primitive RNA genomes may have influenced the ploidy level (the copy

number) and the fragmentation (chromosome number) of the later-arriving DNAgenomes. The early RNA genomes were very fragile and prone to degradation, andthe inaccurate replication processes accumulated multiple mistakes in their se-quences. For these reasons, the genomic components did not grow very large. Inorder to accumulate more coding capacity, the genomes should have been com-posed of multiple short components. To avoid the loss of genetic information dueto high mutation rates, the cells should have maintained more than one copy ofeach genomic component, and thus diploid (or maybe multiploid) rather thanhaploid (prokaryote-like) genomes should have been used (although one has tobear in mind that prokaryotes also normally maintain several copies of theirgenome in each cell). The earlier RNA-genome strategy may have been maintainedafter conversion to the DNA form, suggesting that the earliest cellular genomesshould have been composed of multiple, short, linear components, each presentedin more than a single copy.It is not clear whether the LUCA had evolved, as yet, to the DNA stage, or

whether the transition from RNA to DNA genomes occurred separately in the threedifferent lineages after their separation from the LUCA. Later conversion fromRNA to DNA genomes may be supported by the fact that different types of DNA



Table4.3

Exam

ples

ofpresen

t-da

yRNAcatalystsan

dotherfunction

alRNAs.

RNA

Function

Distribution

Putative

occurren

cein

theRNA

orRNPworld

Ribosom

alRNAs

Translation:structuralan

dcatalytic

Ubiqu

itou

sYes

mRNAs

Carriersof

thegenetic

code

Ubiqu

itou

sYes

tRNAs

Translation:A

minoacid

tran

sport

Ubiqu

itou

sYes

tRNA

Aminoacid

metabolism

Ubiqu

itou

sYes

tRNA

Replicationprim

erRetrotran

sposon

s,retroviruses,

pararetroviruses

Possibly

Telom

eraseRNA

tRNA-like

prim

erforchromosom

een

dsynthesis

Eukaryotes

Yes

RNaseP

tRNAmaturation

Ubiqu

itou

sYes

snoR

NAs

rRNAprocessing

Eukaryotes,som

eArchaea

Yes

RNaseM

RP

rRNAprocessing

Eukaryotes

Related

toRnaseP

GroupIself-splicingintron

smRNAsplicing

Eukaryotes,som

eProkaryotes

Possibly

GroupII

self-splicingintron

smRNAsplicing

Eukaryotes,som

eProkaryotes

Possibly

srpR

NA

Protein

tran

slocation

Eukaryotes,som

eArchaea

Yes

vaultRNA

Not

know

n–Protein

tran

slocation?

Eukaryotes

Possibly

G8RNA

Maintenan

ceof

ribo

somal

apparatus

atelevated

temperatures

Eukaryotes

Probably

Ham

merheadan

dhairpin

ribo

-zymes

Self-cleavage

andlig

ation

Viroids

andsatRNAs

Probably

Sou

rce:Mod

ifiedfrom

Jeffares

etal.1

998.

polymerases are utilized by Bacteria and by Archaea and Eukarya. Also, if the RNAgenomes were stabilized via methylation of the 2’ hydroxyl groups of the ribosemolecules, as suggested by Poole, it is conceivable that the RNA genomes mighthave developed to be fairly large, gaining significant coding capacity. Such RNAgenomes may have been adequate to support self-sustained cellular life and toproduce codes for the ribonucleotide reductases, thymidylate synthases, and re-verse transcription enzymes eventually needed to convert the ribonucleotides intodeoxyribonucleotides and RNA sequences into DNA. Forterre suggests that thoseDNA-producing enzymes and, consequently, DNA genomes were invented severaltimes to establish DNA-based viral genomes colonizing the RNA cells and that theywere transferred from those to the RNA-based host cells, in three separate transferevents, to establish the three DNA-based domains of life.Woese has suggested that at the earliest stage of evolution, when the genomes

were still very small and unstable, the fully functional genetic information couldnot exist in individual discrete organisms or genomes. He suggests that these earlygenomes instead formed a diverse community of organisms that dynamicallyinteracted with each other, exchanging, testing, storing, and evolving alternativegenomic sequences. Woese calls these early life forms “progenotes,” which de-scribes the evolutionary stage preceding the fixed genomic life forms, or the“genotes.” Again, it is not clear whether such progenotes would have had a DNAor an RNA genome; maybe they could have been characteristic both before andafter the transition from RNA to DNA genomes.

4.4“Life” in the RNA–Protein World: Issues and Possible Solutions

LUCA appears to have been a fairly complex and well-established organism – butfrom where did this complexity arise? Information flow from DNA into mRNA andthen into proteins (Fig. 4.5) demands multiple functions in between; therefore, it iscommonly thought that the whole genetic machinery had to evolve from a simplersystem. It is supposed that the genetic system preceding the DNA genomes wereRNA genomes, which could have functioned as information storage media and astemplates for translation. It is thought that the protein synthesis became estab-lished at the time of the RNA genomes and that the appearance of the proteincatalysts then allowed the “invention” and establishment of the DNA genomes.Thus, present-day DNA–RNA–protein life would have been preceded by lifecomposed of RNAs and their encoded protein products – or by RNA–protein(RNP) life.At the earliest stages, when the genetic code was translated into protein products,

or the genetically encoded proteins were “invented,” both the codes and theirexpression system were certainly very primitive. The codes had not yet evolved tocode for specific functions, and also the translation system was very inaccurate.Maybe only a few of the currently known amino acids were used. The system wasable to produce only a few short, nearly random polypeptides. The polypeptides had

4.4 “Life” in the RNA–Protein World: Issues and Possible Solutions 105

not been adapted to specific functions, but maybe some of them could bind to RNAand function as scaffolding or structural proteins, similar to present-day chaper-ones. Such structural proteins may still have been quite useful in stabilizing theRNA genomes and in holding them in suitable three-dimensional structures toenhance their catalytic properties. Such structural proteins probably assisted in themost essential functions of the RNP world, i.e., in the replication of the RNAs. Thehigh mutation rate produced more functional gene products, and in due coursesome proteins appeared that actually catalyzed the replication of RNA genomes.

4.4.1Evolutionary Solutions

The early enzymes were still very inefficient and prone to errors. Therefore, eachtime the genomes were replicated, considerable portions of the nucleotides werecopied wrong and the genetic information was altered. If the sequences mutatedtoo much, it was changed into a non-functional form, the gene was no longermaintained, and the information was totally lost. This critical level of accumulationof errors has been defined by Manfred Eigen as the “error threshold” and is nowknown as the “Eigen limit.” The number of incorrectly copied nucleotides in-creased with the genome length; the longer the genomes, the easier they accumu-lated fatal levels of mistakes. Thus, only fairly short genomes (or genomic compo-nents) could be maintained by this very error-prone replication.Eigen has demonstrated how the evolution of small genomes (e.g., viral ge-

nomes) functions in a cyclic fashion, where repeated improvements of differentsynergistic functions lead to very efficient improvement of fitness and adaptationto new conditions. As described by Poole, this cyclic adaptation and genome-building model seems applicable for the gradual improvement of the RNP organ-isms: the new sequence variants encoded for improved replicase proteins or newcomponents for the translation machinery. These produced better replicase mol-ecules and thereby improved the accuracy of the replication. This again allowed themaintenance of longer genomes – and the increasing coding capacity allowed forthe production of new components for the replication and translation machineries.


Fig. 4.8 Darwin–Eigen cycle demonstratingthat Darwinian selection for improved repli-cation and translation allowed maintenanceof larger genomes, and these again allowedfor improved replication and gene expression.Thus, the increasing genome size, new genefunctions, and improving replication andtranslation fidelity have mutually enhancingeffects on the evolution of complexity (adaptedfrom Poole et al. 1999).

Thus, Darwinian selection for more accurate replication and the correspondingincrease of the genome size (determined by the Eigen limit) together enhanced theevolution towards more complex genomes (Fig. 4.8).

4.4.2Solutions Found in the Viral World

It is of interest that present-day single-stranded (ss) RNA viruses possess multiplefeatures that seem similar to the properties of a hypothetical early RNP organisms.As in the RNP organisms, the viral genomes are composed of short linear RNAsthat code only for a few necessary gene products. The total length of RNA virusgenomes seems to be limited by both the fragility of the RNAs and the Eigen limit(the avoidance of accumulating too many errors by inaccurate replication); thus, atthe present time the longest ss RNA virus genomes – those of the coronaviruses –contain about 30 000 nucleotides. The smallest viral genomes, – those of theleviviruses – are only about 3 500 nucleotides long and code only for three proteins,namely, the replicase protein, the coat protein, and a maturase protein to interactwith the host. These seem to make the minimal protein set required for sustainableviral genomes. In many viruses the replicase proteins are divided in two separatecomponents, the helicase and the replicase, apparently because those proteins needto be produced in very different amounts.The coat protein is required to enclose the RNA and to protect it from degrada-

tion. All viruses encode one or more of other gene products to interact with theirhost cells – mainly in order to suppress the host defense functions – but it appearsthat in principle the replication and the protective functions are the most importantrequirements for viral survival. This may also indicate how important theseproteins may have been to the early RNA replicators.Viruses maximize the use of their limited genomic sequences – they use them in

the most efficient way. They contain a minimal amount of non-coding sequences,and they do not “invest” any coding capacity for producing regulatory proteins,which are so essential for cellular life. Many viruses regulate their essentialfunctions – initiation of replication and translation – by short and simple sequen-ces at the termini of the RNA genomes and by interactions between RNA loops andsequences. With such RNA interactions, some viruses are capable of dedicatingtheir genomic RNAs to function in either the replication or the translation mode,which avoids collision of the two opposite processes.Being parasites of the cellular world, RNA viruses make their living in a chemi-

cally rich environment: the host cells provide all the building blocks of the macro-molecules (the nucleotides and the amino acids) and the translation machinery foruse by the viruses. Likewise, the early RNP organisms had to live in a similarenvironment, because they had no means for synthesizing their own buildingblocks. Through their evolutionary history, the RNA viruses have become veryefficient in their replication and in their adaptation to their own specific hostorganisms. Indeed, in spite of their ultimately minimal size, the RNA viruses arevery successful. There are many more species of viruses than there are cellular


species, and each cellular species may be infected by several different viral species.It is possible that the (fully evolved) RNP-based life forms were efficient andsuccessful replicators. Apparently they had to be quite advanced in order toproduce adequately large genomic pools to give rise to DNA-based life and cellularorganisms. Some of the early RNP-based replicators may have survived to form thebase for the massive variation of present-day viruses.

4.5“Life” Before the Appearance of the Progenote

4.5.1The Breakthrough Organism and the RNA–Protein World

The first protein-mediated functions initiated evolution towards more and morecomplex biochemistry. Therefore, the initiation of genetically encoded proteinsynthesis has been the key step in the development of any more-advanced life.This event has been considered so essential that Poole and coworkers have namedthe first creature that produced proteins the “breakthrough organism.” But howcould this hypothetical breakthrough organism break through – or, how might ithave come into existence in the first place?Clearly, it had to evolve from simpler systems through a cascade of improving

stages. It was required that it be able to synthesize mRNA-like translatablesequences and to run a primitive translation machinery consisting of ribosomes,tRNAs, and amino acids. Because protein synthesis did not exist prior to this time,the assembly or function of this primitive translation machinery could not havedepended on any specific proteins. Thus, the early translation reactions had to becatalyzed by the existing RNAs alone. This is theoretically feasible because in all thepresent-day life forms, the formation of the peptide bonds between amino acids isspecifically mediated by one RNA component of the ribosomes. Different naturalor in vitro–selected RNA molecules may catalyze many other reactions (for thenatural ribozymes, see Table 4.3). For instance, ribozymes have been found thatcan mediate the amino acylation of tRNAs. Thus, according to experimental data, itmay be postulated that mere RNA components were able to mediate the earliesttranslation process.

4.5.2Primitive Translation Machinery

A logical requirement for the existence of RNA-based translation machinery is thatthis machinery itself was initially generated and maintained in a protein-independ-ent manner. Present-day ribosomes are massive complexes, containing either three(in prokaryotes) or four (in eukaryotes) RNAs that vary in size from 120 to 2 904nucleotides. The genes coding for these RNAs take, together with their interveningsequences, more than 7 500 nucleotides of genomic sequences. It is clear that the


earliest RNA components were not as long as they are today. As mentioned inSection 4.4.1, the error-prone replication systems produced only fairly short RNAstrands that are estimated not to have exceeded a few hundred nucleotides in length.Thus, it is likely that the proto-ribosome had to be composed of short fragments ofRNA that jointly formed one functional complex. This may still be evident inpresent-day ribosomes, because their interaction with tRNAs may be mimicked bya separate small RNA analogue of the ribosomal RNA sequence and because peptidebond formation is catalyzed by a specific adenine in the core of the ribosomal RNA.Thus, it seems likely that the present-day ribosomal RNAs (rRNAs) developed via acombination of previously existing, small functional subunits.

4.5.3Origin of Ribosomes

Even if the early ribosomes were formed of small separate RNAs, their mainte-nance required that they be reproduced fairly accurately. The mere existence ofsuch a functional complex required that it had evolved gradually from somesimpler structures – which again had been maintained and selected for their

4.5 “Life” Before the Appearance of the Progenote 109

Fig. 4.9 Model of the early function of the proto-translationmachinery as RNA replication complex (from Poole et al. 1998,with permission from the publisher).

preexisting function(s). The most important function at this stage would have beenthe maintenance of the existing sequences, namely, the replication of RNAs. Pooleand coworkers have proposed that the original function of the proto-ribosomalcomplex was the replication of RNAs. According to their model, the early proto-ribosomes extended the complementary RNA strand on the RNA template byligating nucleotide triplets (corresponding to present-day anticodon loops) broughtinto the reaction by tRNAmolecules or their primitive precursors. This means thatearly replication was mediated by ligation rather than by polymerization. Incorpo-ration of nucleotide triplets rather than single nucleotides had the advantage ofallowing higher affinity and longer-lasting annealing of the incoming nucleotidesto the template. This allowed more time for the very slow RNA catalyst to performthe ligation (Fig. 4.9).According to this model, it is conceivable that amino acid acylation of the incom-

ing tRNAs was a significant step in the early replication process. The covalentbinding of the amino acids to the -CCA terminus of the tRNAs might have chargedthese molecules with energy, which might have been released by the detachment ofthe amino acid during the polymerization. This process might have been used todrive the polymerization. On the other hand, it is conceivable that the positivelycharged amino acids allowed the proper confirmation (tight folding) of the primitive(negatively charged) tRNAs and/or allowed their binding to the replicase complex.Release of the amino acids from the tRNAs might then have caused a conforma-tional change allowing for the release of the used tRNA from the complex.In any of these scenarios, the interaction between template RNA, ribosome, the

“triplet-reading” anticodons of the tRNAs, and the amino acids would have alreadybeen established at the early RNA replication function, prior to the invention ofprotein synthesis. Peptide bond formation might have been initiated as a sponta-neous reaction between the amino acids brought to close proximity by the incom-ing tRNAs. However, later conversion of the whole replication machinery into atranslation function is difficult to conceive – many things would be have beenrequired to change. For example, the hypothetic cleavage and ligation of thenucleotide triplets from the tRNAs and into the growing chain of RNA neededto be stopped and replaced by peptide bond formation. However, it is conceivablethat the introduction of protein synthesis made these changes possible, as itprovided protein catalysts for replication and a strong selection for the use ofribosomes for translation. Both processes, translation and replication, had to bemade to function on the same template in opposite directions. The function of thesame template in both replication and translation seems not to be a major obstacle,as it occurs in all present-day viruses in a coordinated and regulated fashion.Another model for the early role of tRNAs proposed byWeiner andMaizels is the

terminal taging of the replicating RNAs. These terminal tags would have func-tioned as the selective binding and initiation site of the replicase and thereby wouldhave helped to replicate the genomic ends correctly. This hypothesis is supportedby the fact that many present-day viruses have tRNA-like 3’ termini and thetelomerase enzyme that synthesizes the ends of the eukaryotic chromosomesfunctions on a tRNA-like template.


4.6The RNA World

Logically, it is necessary to assume that prior to the invention of protein synthesis,all reactions required for maintenance of macromolecules – and for their evolutiontowards life – had to be mediated by molecules other than proteins. Present-dayRNA chemistry has demonstrated that different RNA molecules (either naturalones or selected in vitro) may mediate several different catalytic activities, althoughthe RNA catalysts typically function less efficiently than protein enzymes, i.e., at amuch slower rate (Fig. 4.2). Such molecules are called RNA enzymes or ribozymes.Most of the naturally occurring ribozymes mediate cleavage and ligation reactionsof their target RNAs (Table 4.3). The smallest ribozymes contain about 50 nucleo-tides and occur in the RNAs of viroids and viral satellite RNAs, while complexribozymes capable of many different catalytic functions can be artificially producedby in vitro selection.It must be emphasized that the functionality of the RNA catalysts is based on the

sequence information. The information does not code for any protein products, butit dictates the folding of the RNA into secondary structures that can recognize theirsubstrates and cause the desired reactions. Figure 4.10 shows the three-dimen-sional folding structure, the so-called hammerhead structure, of the smallestnatural ribozymes, which are composed of about 50 nucleotides.Figure 4.11 gives an example of the evolution of an RNA polymerase ribozyme,

as mediated by in vitro selection steps. The class I ligase ribozyme catalyzes thejoining of the 3’ end of an RNA strand to the 5’ end of the ribozyme (Fig. 4.11 a);the class II ligase ribozyme catalyzes the addition of three nucleotide 5’ triphos-phates (NTPs) to the 3’ end of the primer, directed by an internal template

4.6 The RNA World 111

Fig. 4.10 Three-dimensional folding structure(so-called hammerhead structure) of the small-est natural ribozymes. These self-cleaving and-ligating structures occur in several viroid andviral satellite RNAs and are composed of about50 nucleotides.

(Fig. 4.11 b); finally, the class I–derived polymerase catalyzes the addition of up to14 NTPs on an external RNA template (Fig. 4.11 c).The hypothetic stage of early evolution, when all biochemistry was mediated by

different RNA catalysts, is called the RNA world. Invention of genetically encodedproteins brought out the new, protein-based biochemistry that soon replaced RNA-mediated catalysis. A curious example of this transition to protein-mediatedfunctions is that still today some proteins functioning in the regulation of trans-lation – namely, some translation elongation factors – are folded into a secondarystructure similar to that of the tRNAs. Apparently, after the RNA genomesaccumulated adequate coding capacity, the protein enzymes were able to convertthe RNA genomes to DNA form. Being much more stable than the RNAs, thesecould evolve into much larger sizes and superior coding capacity.With these immense improvements in biochemical functions, the original RNA-

mediated biochemistry might have disappeared without leaving a trace. However,this did not happen, as we do still have some clear molecular relicts, or molecularfossils, that apparently have been conserved from the RNA era into present-day life.The most convincing molecular fossil from the RNA world is that the primarygenetic code is still translatable only from RNA sequence (DNA exists only as aninformation storage system, comparable to a hard disk, containing all the data butno running program for translating this information). Further, the translationreaction, or the formation of the peptide bond, is still mediated by one RNAcomponent of the ribosomes, and the tRNAs still bring the amino acids into thetranslation reaction. Several other small functional RNAs exist in present-day cells(Table 4.3) and also may be functional relicts from the early RNA era.As mentioned in Section 4.3, some of these RNA catalysts – particularly those

that function in the maturation of different RNAs, especially small nuclear RNAsand nucleolar RNAs – as well as RNA-containing telomerase enzymes still occur in


Fig. 4.11 Evolution of an RNA polymeraseribozyme mediated by in vitro selection steps.(a) The class I ligase ribozyme catalyzes thejoining of the 3’ end of an RNA strand (openline) to the 5’ end of the ribozyme; (b) theclass II ligase catalyzes the addition of three

nucleotide 5’-triphosphates (NTPs) to the3’ end of the primer, directed by an internaltemplate; (c) the class I–derived polymerasecatalyzes the addition of up to 14 NTPs on anexternal RNA template (from Joyce 2002, withpermission from the publisher).

the eukaryotic organisms (Table 4.3). This suggests that those (slow) RNA-medi-ated functions have been maintained in eukaryotes from the times of RNA-basedlife. In prokaryotes, many RNA-processing functions have been replaced by pro-tein-catalyzed functions, apparently due to their adaptation to faster replication andto more efficient RNA processing, particularly in hot environments. For thesereasons it might be thought that the eukaryotic genome type – although expandedto huge sizes and complex gene sets over time – would be of a more ancient typethan the small and sophisticated prokaryote genomes.

4.6.1Origin of the RNA World

4.6.1.1 Prebiotic Assembly of PolymersIn order to get the functional RNA world started, preexistence of RNA polymerswas required. These RNA polymers supposedly appeared by spontaneous assemblyor polymerization of nucleotide monomers. They had to accumulate to significantamounts, and be of considerable length and variation, to ensure that this randomcollection contained some (or even one) that had the potential of copying itself and,later, of copying even other RNAs.The prebiotic, i.e., spontaneous, polymerization of RNA nucleotides is difficult to

explain with known RNA chemistry, because nucleotide polymerization requiresenergy and does not happen easily (see Chapter 3). It has been intensively studied –e.g., in the laboratory of James Ferris – and in these optimized conditions,polymers of about 40–50 nucleotides were produced. Such polymerization resultshave been obtained by allowing activated nucleotides to react in aqueous solutionin the presence of clay minerals, which significantly enhanced the polymerization.The enhancement by clays is caused, assumedly, by their fine-layered structure,composed of mineral grains with di- and trivalent positive charges. Those cationicsurfaces bind and immobilize the negatively charged nucleotides, placing them insuitable positions to promote their reactions with each other. Further on, bindingto the clay surfaces significantly stabilizes the ready-made RNA polymers, whichotherwise would be very easily degraded by hydrolysis.The group of Deamer reports that another environment that promotes RNA

polymerization, although to a lesser extent than clays, is the eutectic (very cold) icesolutions; an icy environment is also known to promote the ribozyme-catalyzedligation of RNAs. The liquid water phase remaining in between ice crystalsconcentrates the precursors effectively, and the low temperatures help to slowdown the reacting components to allow the formation of the phosphodiester bondsbetween nucleotides.For building the nucleotide polymers, the nucleotides need to be linked to each

other via phosphodiester bond between the 3’ and 5’ carbons of the adjacent sugars(Fig. 4.3). For this, the nucleosides first have to be phosphorylated at their5’ carbon. In the early world this was problematic because soluble phosphateswere not readily available. It is possible that the inorganic phosphate dissolved inlow amounts from calcium phosphate (hydroxyapatite) mineral or from volcani-


cally produced linear polyphosphates, or from their breakdown products, andphosphorylated nucleosides to nucleotides. But this reaction is difficult and mightoccur only in the presence of urea, ammonium chloride, and heat.Polymerization of the nucleotides requires that they be activated by some high-

energy bond at the 5’ position to provide energy for the uphill reaction. In present-day life, this binding energy is obtained from the hydrolysis of the triphosphatemoiety, but this was not adequate in the prebiotic world because triphosphatesalone do not promote (non-enzymatic or non-catalyzed) polymerization. Therefore,it seems that the nucleotides had to be charged with other available molecules, suchas amino acids, bound with high-energy bonds at the 5’ position of the phosphory-lated nucleotides. The most effective activating groups, now commonly used forthe polymerization experiments in laboratories, are the different phosphorami-dates, such as phophoramidazoles. These compounds are formed from nucleoside5’ polyphosphates and amines or imidazoles; but such complex activating groupsmight not have been available in the prebiotic environment.A further complication in the polymerization of ribonucleotides is that in a

mixture of monomers, several different reactions take place. To make a functionalpolymer, the monomers must form the mono-phosphodiester linkage exactlybetween the 3’ and 5’ carbons of the adjacent nucleotides. However, the ribosering has reactive groups in carbons at positions 5’, 3’, and 2’ (Fig. 4.3). In prebioticconditions all these groups could react with each other, and cyclic compoundscould be formed between the 2’ and 3’ OH groups. Furthermore, the phosphatemolecules might have formed different polyphosphate linkages between differentcarbons. All these varying bonds would have produced dead-end products forfurther polymerization. It is still unclear what kind of conditions promoted thenucleotides to react in an orderly fashion to produce only the correct, 3’-to-5’-linkedRNA polymers (Fig. 4.4).

4.6.1.2 The Building Blocks of the RNA WorldFor synthesis of nucleosides, the purine bases adenine and guanine (A and G), thepyrimidine bases cytosine and uracil (C and U), and the D-isoform of cyclic ribosesugar are needed. Prebiotic synthesis and assembly of these nucleoside buildingblocks have been intensively studied by groups of chemists led by Gerald Joyce,Stanley Miller, Leslie Orgel, and Alan Schwartz. The prebiotic synthesis of thesecomponents, as well as the prebiotic synthesis of their small organic precursorssuch as CH4, NH3, CH2O, CNH, CN2H4, C3NH, CH2O, CN2H4O, and SH2, iscovered in Chapter 3.Provided that ribose sugar and the nucleobases were available, further on the

bases had to be covalently linked in �-orientation with the 1’ carbon of ribose toform nucleosides. This reaction may be activated by heating and it produces purinenucleosides, although with very low yield. Routes for prebiotic synthesis of pyr-imidine nucleosides are not well known, but they may be feasible via multiplesugar phosphate intermediates. Recently, a completely different route has beenfound, where Æ-D-cytosine was produced directly from ribose sugar and hydrogen


cyanide. This efficient reaction thus produced cytosine, even if of the wrongisoform, and it also converted the existing (unstable) ribose into a stable form.Prebiotic synthesis of nucleotides would have yielded a racemic mixture of a

variety of different nucleotide analogues, both in Æ and � and in L- and D-isoforms.A spontaneous polymerization reaction of such (randomly) phosphorylated nu-cleotides would have been very slow and would have led to a wide variety ofdifferent linkages, formed between the whole variety of different nucleotide ana-logues and isoforms. Such randomly linked oligomers or polymers would not havebeen extendable or functional as templates for replication.Altogether, prebiotic formation of RNA nucleotides and their polymers, starting

from small molecular precursors such as HCN, NH3, CH2O, CH4, PO43–, or H2O,

involves so many unlikely or adverse chemical steps that many chemists havespeculated that RNA synthesis had to be preceded by simpler chemical polymers –or by nucleic acid analogues whose backbone is composed of non-chiral structures.Polymers proposed as hypothetical predecessors of the RNA world include peptidenucleic acids (PNAs) with a peptide as backbone, threose nucleic acids (TNAs), andpyranosyl-derived nucleic acids (p-RNAs) (see Chapter 1). If any of these polymerswas a direct precursor of present genetic material, then it must have been possibleto transfer the information by copying or transcription from this molecule intoRNA or DNA sequence, which indeed has been experimentally demonstrated forPNAs. However, the role of other polymers in the early steps of molecularevolution does not seem very plausible, because the central molecules of earlylife (the ribosomes and tRNAs) are based solely on RNA molecules.To find possible solutions for the appearance of the nucleotide-based (very

complex) genetic information, Cairn-Smith (1982) has postulated that instead oforganic polymers, entirely different molecules, such as minerals, may have con-tained the earliest pre-genetic (replicating) information. Still, it is not clear how anyspecific information would have been coded in the crystal structure of mineralsurfaces, or how these would have been converted to be biologically significant.Little is known, as yet, of what the available starting materials were, what theconditions were where the prebiotic chemistry took place, and what chemical andphysical reactions and selection processes were driving the increasing complexityof the early polymers (see also Chapter 1).

4.6.1.3 Where Could the RNA World Exist and Function?The question of the possible location and conditions of the proposed RNA world isvery difficult. It is assumed that the initial RNA polymers were formed by randompolymerization of nucleotides, but this scenario requires that the nucleotides hadto be initially available in the environment. Further on, for the synthesis ofnucleotides, their precursors – ribose sugar, purines and pyrimidines, and phos-phate molecules – had to be available. For the prebiotic synthesis of those com-pounds, their precursors or the small organic molecules such as CH2O, CNH,CN2H4, and HNCO had to be available in adequate amounts. To drive repeatedpolymerization reactions, leading to significant accumulation of the products


(adequate for starting a whole new polymerization and replication network), a long-term, high-level supply of nucleotides would be required.The prebiotic synthesis or at least the accumulation of nucleotides would need to

happen in conditions where, further on, the nucleotides could spontaneouslypolymerize. The conditions also should have been adequately gentle to maintainthe polymers intact. The prebiotic synthesis of some of the precursors happenspreferably in cold or mildly warm conditions (synthesis of nucleic acid bases),while other steps require heat (nucleoside formation and phosphorylation). So it isconceivable that the locations for the different steps may have been temporally orlocally separate.The polymerization of nucleotides needs to take place in an aqueous environ-

ment because the nucleotides are water-soluble and liquid water is needed to carrythem into the reaction site. However, water efficiently reacts with the RNApolymers to hydrolyze the phosphodiester bonds, which breaks up the polymers.The hydrolysis reactions occur faster at higher temperatures; therefore, cool, closeto freezing temperatures would be more suitable for preserving RNA polymers.A further complication arises with the templated polymerization – meaning the

copying or replication of existing RNA strands. Because the phosphate groupsforming the phosphodiester bonds carry a negative charge of –1, the total chargeof the polymer is highly negative. In the templated replication, the complementarystrand is assembled on the existing template by hydrogen bonding between thecomplementary nucleotides (A to U andG to C) (Fig. 4.4). For stable assembly of thecomplementary strand, the negative charges of the phosphates need to be neutral-ized by an adequate level of soluble cations (positive ions). This neutralizationtogether with the hydrogen bonding of the bases leads to a stable assembly, andthe double-stranded product is closed for any further assembly of new strands on thesame templates. Thus, the double-stranded structure could be a dead-end product.To avoid this, some energy input or radical change of environment – e.g., by

dilution out of the cationic ions or warming up of the solution – would be needed toopen up the double helix. Lathe (2005) has proposed that alternating conditions oflow and high salt concentrations (as in tidal pools) would be needed to drive theassembly and separate the daughter strands. Brown and coworkers have experi-mentally shown that efficient melting (i.e., separation) of double-stranded nucleicacid strands can be obtained by convection-driven cycling of molecules in micro-compartments located in steep temperature gradients, such as the tiny compart-ments in the FeS precipitate mounts of hydrothermal vents.Still another putative environment that might have driven prebiotic chemistry

and the assembly of macromolecules, possibly including polymers, is the sandy orsilty beaches washed by the ocean tides. Bywater and Conde-Frieboes (2005) haveproposed that in these locations the ocean water would have brought in theprecursors for the reactions, and these might have been bound, by hydrogenbonding or ionic forces, to the cationic minerals in the clay and sand. Small dryingponds might have provided the concentration mechanism for the compounds, andthe subsurface layers of sand might have provided protection against UV radiation,as well as size-based fractionation and concentration by chromatographic filtration.


The clay-like minerals would have been suitable catalytic surfaces for the assemblyof nucleotide polymers. The repeated washes by new waves or tides might haveprovided the cyclic dilution effects needed for the separation of the replicatingnucleotide strands, as proposed by Lathe.

4.7Beginning of Life

The above discussion should indicate that the origin of life was by no meanssimple. Rather, it should have been a procession through multiple stages ofspontaneous – but most often uphill – reactions of molecular chemistry andevolution towards cellular life. Within this procession it is difficult to determinewhen life actually started. It seems that there was a stage where the developingsystem was not yet clearly alive, and also no longer clearly lifeless, but swaying inbetween different directions of development in a type of bifurcating stage. Such athreshold level could have been achieved when the first sequences could replicatethemselves but when there were no biosynthesis pathways, as yet, for any of theprecursors or building blocks for making more of the same molecules. The systemwas modified and adapted by a selective evolution, but it was still wholly dependenton the supply of complex materials from its environment. It is conceivable thatsuch a threshold stage could have developed in several directions: one, for instance,to produce the semi-living (replicating but not autonomous) viral world andanother to produce autonomous cellular life. Parasitic and synergistic interactionsalso evolved – the viruses ending up as parasites of cellular life – but the earlymolecular interactions may have been more varied.The question of the beginning of life is related to how we define life. Life, as we

now know it, is very complex and versatile, but the definition should include justthe very minimal and first features that were required of a system to become alive.Andr� Brack has defined primitive life as an aqueous chemical system able totransfer its molecular information and to evolve (see Chapter 1). Eigen hasdescribed life as phenomena in the multidimensional information space, wherethe species – or quasi-species – form as their genomic sequences accumulate in theproximity of the optimal or best-adapted sequence, at so-called “fitness peaks.”Both these descriptions emphasize the information-driven nature of life, themaintenance of information via replication, and accumulation of new informationvia natural selection and evolution.In a reductionist way, it might be claimed that genomic information is the

essential part of life and that the cellular structure serves only as a vehicle tomaintain and renew the information. But the cellular structure has played a centralrole in the formation of information: the accumulated information just reflects theneeds of the cells, and the optimized information is determined by the adaptationof the cell to its environment.The very initial functional information appeared by accident, as a random

sequence was able to replicate itself. The further accumulation of information

4.7 Beginning of Life 117

took place via improvement of that very function. When the system grew andevolved, new functions were “invented” that allowed the system to survive better inits environment. The selection, or genetic adaptation, was mediated via differentinteractions. Intracellular molecular interactions were, and still are, of essentialimportance, as were the interactions of the cell with its surroundings, with themembers of its own species, and with the whole surrounding ecosystem. Theseinteractions are the driving force for the accumulation of genetic information.Even the simplest cellular life is mediated via multiple biochemical reactions

driven by energy conversion reactions and, ultimately, by energy drawn from asuitable energy source. With these, life achieves a remarkable organization ofmatter and energy. The cellular structure is essential for the containment of allthese reactions and for the assembly of the organized structures.Thus, life is indeed based on genetic information and on evolution, but the third

essential party in the assembly of life is its cellular form. The cell and its inter-actions with the environment – and, on the other hand, its separation from theenvironment –build the entity that has allowed the accumulation of informationand that has facilitated evolution, and the self-sustained existence of the organism.Its existence still depends on suitable energy sources and availability of nutrients,i.e., on the life-supporting environment. A cell, adapting in its life-supportingenvironment, was the last defining requirement for the establishment of life aswe know it on Earth.

4.8Further Reading

4.8.1Books

Brack, A. The Molecular Origin of Life.Assembling Pieces of the Puzzle, CambridgeUniversity Press, Cambridge, 417 pp.,1998.

Cairn-Smith, A. G. Genetic Takeover and theMineral Origins of Life, Cambridge Univer-sity Press, Cambridge, 1982 (http://origin-oflife.net/cairns_smith/).



Abe, Y. Physical state of the very early earth,Lithos 1993, 30, 223–235.

Berclaz, N., Muller, M., Walde, P., Luisi,P. L. Growth and transformation of vesiclesstudied by ferritin labeling and cryotrans-mission electron microscopy, J. Phys. Chem.2001, 105, 1056–1064. (http://www.plluisi.org/)

Biebricher, C. K., Eigen, M. The error thresh-old, Virus Res. 2005, 107, 117–127.

Bywater, R. P., Conde-Frieboes, K. Did life beginon the beach? Astrobiology 2005, 5, 568–574.

Chang, I.-F., Szick-Miranda, K., Pan, S., Bailey-Serres, J. Proteomic characterization of evo-lutionary conserved and variable proteins ofArabidopsis cytosolic ribosomes, PlantPhysiol. 2005, 137, 848–862.

Chen, I. A., Roberts, R.W., Szostak J.W. Theemergence of competition between modelprotocells, Science 2004, 305, 1474–1476.

Delaye, D. Becerra, A., Lazcano, A. The lastcommon ancestor: what’s in the name, Orig.Life Evol. Biosph. 2005 35, 537–554.

DeDuve, C. A research proposal on the originof life, Orig. Life Evol. Biosph. 2002, 33,559–574.

Deamer, D., Dworkin, J. P., Sandford, S.A.,Bernstein, M. P., Allamandola, L. J. Thefirst cell membranes, Astrobiology 2002, 2,371–381.

Doolittle, W. F. Phylogenetic classification andthe universal tree, Science 1999, 284, 2124–2128.

Eigen, M. The origin of genetic information:viruses as models, Gene, 1993, 135, 37–47.

Ferris, J. P. Montmorillonite catalysis of 30–50mer oligonucleotides: laboratory demon-stration of potential steps in the origin of theRNA world, Orig. Life Evol. Biosph. 2002, 32,311–332.

Forterre, P. The two ages of the RNAworld, andtransition to theDNAworld: a story of virusesand cells, Biochim. 2005, 87, 793–803.

Forterre, P., Confalonieri, F., Charbonnier, F.,Duguet, M. Speculation on the origin of lifeand thermophily: Review of available infor-mation on reverse gyrase suggests that hy-perthermophilic procaryotes are not soprimitive, Orig. Life Evol. Biosph. 1995, 25,235–249.

Gil, R., Silva, F. J., Pereto, J., Moya, A. Deter-mination of the core of the minimal bacte-rial gene set. Microbiol. andmolec, Biol. Rev.2004, 68, 518–537.

Hanczyc, M.M., Szostak, J.W. Replication ofvesicles as models of primitive cell growthand division. Current Opin., Chem. Biol.2004, 8, 660–664.

Jeffares, D. C., Poole, A.M., Penny, D. Relictsfrom the RNA world, J. Mol. Evol. 1998, 46,18–36.

Joyce, G. F. The antiquity of RNA-based evo-lution, Nature 2002, 418, 214–221.

Kanavarioti, A., Monnard, P.-A., Deamer,D.W. Eutechtic phsces in ice facilitate non-enzymatic nucleic acid synthesis, Astrobiol-ogy 2001, 1, 271–281.

Kapp, L. D., Lorsch, J. R. The molecular me-chanics of eukaryotic translation, Ann. Rev.Biochem. 2004, 73, 657–704.

Koonin, E., Martin, W. On the origin of ge-nomes and cells within inorganic compart-ments, Trends Genet. 2005, 21, 647–654.

Lathe, R. Tidal chain reaction and the origin ofreplicating polymers, Int. J. Astrobiol. 2005,4, 19–31.

Lehto, K., Karetnikov, A. Relicts and modelsof the RNA world, Int. J. Astrobiol. 2005, 4,33–41.

Liang, H., Landweber, L. F. Molecular mimi-cry: quantitative methods to study structuralsimilarity between protein and RNA, RNA2005, 11, 1167–1172.

Maizels, N., Weiner, A.M. Phylogeny fromfunction: evidence from the molecular fossilrecord that tRNA originated in replication,not translation, Proc. Natl. Acad. Sci. USA1994, 91, 6729–6734.

Martin, W., Russell, M. J. On the origin of cells:a hypothesis for the evolutionary transfor-mation from abiotic geochemistry to che-moautotrophic prokaryotes, and from pro-karyotes to nucleated cells, Phil. Trans. R.Soc. Lond. B. 2002, 358, 59–85 (also in:www.gla.ac.uk/project/originoflife/html/2001/pdf_files/Martin_&_Russell.pdf).

Mojzsis, S. J., Arrhenius, G., Keegan, K. D.,Harrison, T.M., Nutman, A. P., Friend,C. R. L. Evidence for life on Earth before3,800 million years ago, Nature 1996, 384,55–59.

Orgel, L. E. Prebiotic chemistry and the originof the RNA world, Crit. Rev. Biochem. Mo.2004, 39, 99–123.

Pennisi, E. Is it time to uproot the tree of life,Science 1999, 284, 1305–1307.

Poole, A., Penny, D., Sjçberg, B-M. Methyl-RNA: an evolutionary bridge between RNAand DNA? Chem. Biol. 2000, 7, R207–R216.

Poole, A., Jeffares, D., Penny, D. Early evolu-tion: prokaryotes, the new kids on the block,BioEssays 1999, 21, 880–889.

Poole, A.M., Jeffares, D., Penny, D. The pathfrom the RNA world, J. Mol. Evol. 1998, 46,1–17.

Sanders, P. G.H. Chirality in the RNA worldand beyond, Int. J. Astrobiol. 2005, 4, 49–61.

Schmidt, G., Christensen, L., Nielsen, P. E.,Orgel, L. E. Information transfer from DNAto peptide nucleic acids by template-directedsyntheses, Nucleic Acids Res. 1997, 25, 4793–4796.

Steitz, T. A., Moore, P. B. RNA, the firstmacromolecular catalyst: the ribosome is aribozyme, Trends Biochem. Sci. 2003, 28,411–418.


Tian, F., Toon, O. B., Pavlov, A. A., De Streck,H. The hydrogen-rich early atmosphere,Science 2005, 308, 1014–1017.

Vlassov, A. V., Johnston, B. H., Landweber,L. F., Kazakov, S.A. Ligating activity offragmented ribozymes in frozen solution:implications for the RNA world, Nucl. AcidsRes. 2004, 32, 2966–2974.

W�chtersh�user, G. From pre-cells to Eukarya– a tale of two lipids,Mol. Microbiol. 2003, 47,13–22.

Watson, E. B., Harrison, T.M. Zircon ther-mometer reveals minimum melting condi-tions on earliest Earth, Science 2005, 308,841–844.

Weiner, A.M., Maizels, N. The genomic taghypothesis: modern viruses as molecular

fossils of ancient strategies for genomicreplication, and clues regarding the originof protein synthesis, Biol. Bull. 1999, 196,327–330.

Westall, F. Life on the early Earth: A sedi-mentary view, Science 2005, 308, 366–367.

Woese, C. R. The universal ancestor, Proc. Natl.Acad. Sci. USA 1998, 95, 6854–6859.

Woese, C. R., Kandler, O., Wheelis, M. L. To-wards a natural system of organisms: Pro-posal for the domains Archaea, Bacteria andEucarya, Proc. Natl. Acad. Science USA 1990,87, 4576

Yang, S., Doolittle, R. F., Bourne, P. E. Phy-logeny determined by protein domain con-tent, Proc. Natl. Acad.Sci. USA 2005, 102,373–378.


Question 4.1What are the difficulties in understanding of the origin of life?Question 4.2

What are the building blocks of life and how do they assemble to make functionalcells?Question 4.3

What are the putative steps required for the establishment of self-sustainable life?Question 4.4Explain the RNA world.Question 4.5What kind of conditions might have driven the prebiotic molecular evolution

towards life?Question 4.6What can we say of the LUCA and of the differentiation of the three domains of

life from LUCA?Question 4.7How do you define the beginning of life?


4From Molecular Evolution to Cellular LifeKirsi Lehto

In this chapter, contemporary cellular life is analyzed in order tosee which components are the most ubiquitous and conserved inall life forms and therefore assumed to be the most original func-tional units of life. Molecular analysis of these structures givessuggestions of how they were involved in early molecular evolutionand what functions they may have provided to the early (pre-cellular) replicators. By going backwards, step by step, one seeswhich inventions had to precede each stage of early evolution:genetically encoded proteins had to exist prior to the establishmentof the Last Universal Common Ancestor (LUCA), and RNA repli-cators, or replicating RNA analogues had to predate geneticallyencoded proteins. Special attention is given to the most conservedcomponents of the present life forms, considered to be relicts of theearly RNA world.

4.1History of Life at Its Beginnings

Our home planet was formed about 4.6 billion years ago. The initial conditions onthe young planet Earth were very harsh. The accretion process had heated theprotoplanet, and the temperature of the young planet was further increased by thegreenhouse phenomena caused by the dense atmosphere formed by H2O and CO2

and by continuing impacts from the colliding comets and meteorites. The initialplanet temperature was hot enough to keep the Earth’s crust in liquid form,forming a magma ocean on the surface. As the planet radiated heat, the temper-ature was reduced; when it came down to about 200 �C, with the prevailing highatmospheric pressure, the water vapor precipitated and rained down to formoceans. The dating obtained from the oldest zircon crystals indicates that liquidwater was present on the planet 4.4 billion years ago. The first Earth crust formed



underneath the water. Because of heavy cometary and asteroid impacts, the con-ditions on Earth remained hot and violent for perhaps 500 million years; this timeis called the Hadean period.Conditions during the Hadean period are difficult to investigate because all the

rocks formed during that era have been thoroughly metamorphosed by the tectonicprocesses of the later times. The oldest still existing sedimentary rocks are locatedat Isua, Greenland, and date back to about 3.8 billion years. These rocks containsmall granules of sedimented carbon, which is specifically enriched in the 12Crather than the heavier 13C isotope. The enrichment of the lighter carbon isotope inthese sediments suggests that the carbon was once bound in biologically producedcompounds (see Chapters 1 and 2). The real biological origin of these carbondeposits has been questioned, but other nearly as old samples containing 12C-enriched carbon and fossilized microbial structures have been detected at two otherlocations: in the 3.5-billion-year-old sediments at Pilbara, western Australia, and atBarberton, South Africa. These findings suggest that life was well established, andapparently widely distributed on the Earth, at this very early stage – or soon afterthe heavy bombardment ended and the planet cooled to temperatures conducivefor life. It is not known at what temperature regimes life started. The mostthermotolerant contemporary life forms are known to propagate in temperaturesup to 113�C (see Chapter 5), but the prebiotic replicating macromolecules, and alsothe earliest cellular structures, may have been rather fragile and sensitive forhydrolytic conditions and most likely were not durable in very high temperatures.Since its early start, life has spread and diversified and now occupies all con-

ceivable ecological niches on the Earth (see Chapter 5). During its spread andaccumulation, life has also modified the environment and has profoundly changedthe conditions on planet Earth, including the chemical composition of the atmos-phere, the oceans, and the Earth’s crust. The long-term geological processes oftectonics, volcanism, weathering and erosion, as well as degrading processescaused by life itself, have completely reshaped and mixed multiple times theconditions that prevailed on the early Earth and have abolished most of thechemical and geochemical traces that were formed at this early time. Therefore,there are not any direct data of the conditions that once allowed or induced theorigin of life. It is even not know in what type of locations on Earth – or, potentially,on nearby planetary bodies – life did start. Thus, trying to trace back the veryearliest stages of this process becomes difficult and speculative.However, different scientific approaches may be used to try to resolve what kind

of conditions and what chemical compounds might have driven the life-producingreactions. Clearly, the origin of life has been a very complex process and needs to bestudied in many different fields of science. Astronomy is needed to resolve how theelements, the Solar System, and the planet Earth were formed in the first place.Geosciences are needed to resolve the conditions on the early Earth and thecomposition of the early atmosphere, the ocean, and the crust. Inorganic andorganic chemistry are needed to resolve how the elements, inorganic minerals, andvolatiles may have reacted to form small organic compounds and more complexorganics such as nucleotides and amino acids, which are the building blocks of life.


Further on, the quest is to resolve how these organic molecules may polymerizeand, in particular, how these reactions might conceivably have happened in pre-biotic conditions in the absence of genetically encoded enzymes and biochemicalreactions.Present-day life is solely driven by multiple protein-catalyzed (-mediated) bio-

chemical reactions and complex molecular interactions. The fields of biochemistryand bioinformatics study how these enzymes and other proteins now function andhow they have changed over the evolution of life. These studies can identify thegenetic sequences that are the most conserved (i.e., the oldest and most originalones) in different life forms. Of particular interest here are the reactions that stillare catalyzed not by proteins but by different RNA molecules. Such RNA enzymes(or ribozymes) may be derived from the very oldest life forms or from the erapredating the DNA-protein-based life forms.As a central part of the study of life, different fields of biology study the essential

structures and functions of life; how life reacts and adapts in its environment; andhow all functions are mediated, regulated, and coordinated on the cellular andmolecular level. All these integrated efforts are needed to construct an under-standing of what life is, how it has evolved through times, and, maybe, how itstarted in the first place.It may be assumed that the chemical and molecular evolution towards life

proceeded through a long cascade of different stages, initiated by spontaneousreactions between abundant chemical elements, or the chemical constituents oflife: carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphor (C, H, O, N, S, P). Insome high-energy conditions these elements formed reduced carbon and nitrogencompounds, such as hydrogen cyanide (HCN), ammonia (NH3), methane (CH4),and formaldehyde (HCHO). In suitable conditions these small organic molecules,together with water (H2O), reacted to form the building blocks of life: the nucleicacid bases (purines and pyrimidines), sugars and other hydrocarbons, and aminoacids (see Chapter 3 and Section 4.2). These, again via multiple chemical reactionsand interactions (which are not well understood as yet), formed polymers andmore-complex molecules. Some of the polymers gained the chemical potential tocopy themselves or to replicate, which was the first major transition towards theorigin of life. Replication initiated molecular evolution, which led to the inventionof genetically encoded proteins and, eventually, to the appearance of the firstcellular life forms. From then on, the diversification of life into all the species ofthe biosphere has been covered by Darwinian evolution.This chapter aims to trace back this process in order to visualize the different

stages of the progress from early organic molecules to cellular life forms. Instead ofstarting from the very beginning and progressing upwards, the chapter starts fromthe central features of cellular life as they are known now, because it is known forcertain that this is what eventually came out of early evolution (at the time ithappened, evolution was random and not directed – the outcome could be knownonly after it had happened). Then proceeding backwards, step by step, it discusseswhat types of simpler forms could have given rise to each of the new and morecomplex innovations.


4.2Life as It Is Known

4.2.1The Phylogenetic Tree of Life

Life is characterized by endless complexity. On the visible level one can observe themultitude of genera, species, forms, and individuals, each thriving in their owntypical ecological niches. Cells of higher organisms are differentiated into organsand tissues, which each present their specific form and function even that they allare regulated by the same genome of the same individual. Variation of species andsubspecies in the microbial world is vastly larger than that of the macrospecies. Themicrobial species can be separated into three different domains of life. Single-celledorganisms such as yeasts, ciliates, and flagellates, which do posses a nucleus in theircells, together with all the higher organisms belong in the domain of Eukarya. Thecells that do not posses a nucleus belong to the prokaryotes, which again belong totwo distinct domains, the Bacteria (or by older nomenclature, the Eubacteria) andthe Archaea (older name, the Archaebacteria). These three domains of life (Eukarya,Bacteria, andArchaea) each constitute their own and separate lineages of life and canbe distinguished from each other by multiple genetic and biochemical markers.The three domains of life share a large number of common features that are

ubiquitous to life, or are the same or very similar in all living organisms. It isbelieved that these features were inherited from a common ancestor of all lifeforms, the Last Universal Common Ancestor (LUCA). However, the properties ofLUCA at the time of diversification and the exact sequence of the separation of thethree lines are still unclear. Clearly, the common ancestor has developed through acascade of gradually increasing complexity, and it is not quite clear, which stagewas The Last Common One. As reviewed by Delaye and coworkers (2005), it mighthave been a community of simple precursors of life, the so-called progenotes (seeSection 4.3.2), or even a community of free-living replicating molecules, predatingthe establishment of cellular life. However, recent phylogenetic studies (i.e.,studies of the lineages and relatedness of known organisms through statisticalcomparison of their genetic sequences) by, e.g., the groups of Lazcano andDoolittle, indicate that LUCA was a well-established cell line. The properties ofLUCA will be discussed below.

4.2.2Life is Cellular, Happens in Liquid Water, and Is Based on Genetic Information

From unicellular microorganisms to all higher life forms, all life on Earth iscellular (Fig. 4.1). Prokaryotes are single-celled organisms. The cells are simpleand usually devoid of any internal membrane structures (except for the photo-synthetic cyanobacteria, which possess intensive photosynthetic membranes). Thecells are spherical, ellipsoid, elongated, or rod-shaped (see Chapter 5) and of sizesvarying from 0.1 �m to 600 �m, depending on the species.


All eukaryote cells have intensive internal structure. Cell organelles include• the nucleus (contains the chromosomes or the genomic

DNA);• mitochondria (energy-producing organelles);• the endoplasmic reticulum (internal membranes),• the Golgi apparatus (membranous vesicles for protein pro-

cessing and transport),• lysosomes and peroxisomes (for containment of degradative

enzymes and wastes); and• chloroplasts (photosynthetic organelles; in plant cells only).

The cells of all eukaryotes are very similar to each other, except that the plant cellshave thick and rigid cell walls and contain numerous chloroplasts (or other types ofplastids). Typical sizes vary from 10 �m to several hundred micrometers, but somelarge cell types occur (of a size up to more than 1 m for some nerve cells).Multicellular organismsmay be conceived as tightly bound colonies of individual

cells. The cells are entities contained within the cell membrane, which separates


Fig. 4.1 All life is cellular. (A) Microscopic view of (unidentified)bacterial cells. (B) Scheme of a eukaryotic cell (animal cell on theleft, and plant cell, with a rigid cell wall, on the right) showing theintensive internal structure.

the cell from its environment but also allows sophisticated communication withthe environment. The communication includes the intake of water and necessarynutrients, excretion of waste products, receiving of chemical signals via differentreceptor molecules, and sending off signals via secretion of different molecules.Thus, the cells dynamically communicate with their environment. All communi-cation through the membrane is mediated via specific proteinaceous channels andstructures embedded in the membrane, because the membrane itself is a hydro-phobic barrier and therefore impermeable to water-soluble molecules.Inside the cells, life is a chemical process where multiple biochemical reactions

take place in aqueous solution. Water functions as the solvent and carrier for ionicand polar molecules, and also is a reacting component in many reactions. Wateralso serves as the exclusion medium to allow the lipid molecules to assemble andformmembranes, and as the medium that interacts with proteins, helping them tofold into their three-dimensional forms. Therefore, water provides a suitableenvironment for the different cellular reactions and for the assembly of importantcellular structures. It provides turgor (internal pressure) and strength to the cells.Water is such an essential environment and requirement for all the life functionsthat it seems likely that the origin of life had to happen in an aqueous environment(see Chapter 1).Proteins, or gene products, have a multitude of essential roles in the cells. They

form several different structures, such as the cytoskeletons in eukaryotes, com-ponents of cell walls, and the porous structures in cell membranes. They regulatereactions such as gene expression and genome replication, and they function insignal transduction by interacting with different target molecules. Still anotherarea where proteins are essential for life is in the (regulated) catalysis of all thereactions going on inside the cells. Most cellular molecules are both synthesizedand degraded via multi-step reaction pathways – and none of these reactionswould happen, at least at any desired rate, without the assistance of proteinaceousenzymes. Even the energy conversion and -releasing reactions have to be medi-ated via enzymatic catalysis so that they happen in a controlled and regulated


Fig. 4.2 Chemical reactionrates in dependence of sub-strate concentration, with andwithout enzyme catalysis. En-zymes speed up reaction ratesvery strongly as compared tonon-catalyzed reactions andmake them happen efficientlyeven at very low substrate con-centrations. The maximum rateof reaction is reached when theenzyme becomes saturatedwith the substrate molecules.

fashion. The enzymes themselves do not participate in the reactions but associatewith the reacting molecules and hold them in such a conformation that thereaction can proceed. Enzymatic catalysis is capable of raising reaction rates bymany orders of magnitude, from nearly zero to very high, and in practice mostbiological reactions would not happen in physiological conditions without enzymecatalysis (Fig. 4.2).Proteins form the tools and the structures in the cells, and genetic information,

encoded in the genomic deoxyribose nucleic acid (DNA), specifies how these toolsand structures are made. Life depends on the function of the proteins and thus onthe genetic information coding for them. Proteins are composed of long chains ofdifferent amino acids, and the sequence of the amino acids in these chains isdetermined by the genes coding for them. From the DNA, the protein-codingsequences are first copied into ribose nucleic acid (RNA) and from this areconverted into amino acid sequences in peptide chains. RNA is a polymer moleculevery similar to DNA; it is composed of similar nucleotide components, with onlythe small difference of an OH group, rather than H, being connected to the carbonin position 2 (2’) in the pentose sugar ring (thus, the sugar is ribose instead of


Fig. 4.3 Structure of the componentsof genetic material: the nucleic acidbases adenine, guanine, cytosine,thymine, and uracil; the deoxyriboseand ribose sugar molecules; and thephosphate moiety.

deoxyribose) (Fig. 4.3). However, this OH group is very reactive and, differing fromthe DNA, makes the RNA polymers very fragile, unstable, and short-lived.

4.2.2.1 Genetic InformationThe complexity of life extends strongly to the molecular level, i.e., to the nucleicacid and protein level inside the cells. The genetic information is encoded in thegenomic DNA in the sequence of four different deoxyribonucleotides (or, in short,nucleotides), which are the phosphorylated form of adenosine (A), guanosine (G),cytosine (C), and thymidine (T) nucleosides. In RNA, the uridine nucleoside isused instead of the thymidine nucleoside. The nucleosides themselves are formedof the corresponding bases (adenine, guanine, cytosine, thymine, and uracil); ofthese, A and G bases are purines and C, T, and U bases are pyrimidines (Fig. 4.3).The bases are covalently bound to a deoxyribose (in DNA) or ribose (in RNA) sugarto form nucleosides. These are phosphorylated at the carbon at their 5’ position toform nucleotides, and these again are connected into long chains via phospho-diester bonds between the 5’ and 3’ carbons (these are the carbons in positions 3and 5 in the ribose ring) of the adjacent sugars (Fig. 4.4).The number of nucleotides in the genomes varies largely between different

species. The genomes of the smallest prokaryotes are composed of about 0.5 � 106

nucleotides, while the genome of the bacterium Escherichia coli is composed of4.8 � 106 nucleotides. The smallest eukaryotic genomes are about an order ofmagnitude larger, but the more complex ones are many orders of magnitude largerthan the prokaryote genomes. The genome of wheat, for instance, is composed of


Fig. 4.4 Schemes of DNA. (A) The deoxyribonucleotide polymerformed by diester bonds between the 3’ and 5’ carbons ofadjacent nucleotides; (B) the double helix of two DNA strandsshowing the base pairing of the nucleic acid bases.

about 17 000 � 106 nucleotides, the human genome of 3 400 � 106 nucleotides, andthat of the fruit fly of 97 � 106 nucleotides (Table 4.1). Further, the number of genesvaries a lot, being about 400 in the smallest endosymbiotic bacteria (Buchneraaphidicola) and some hundreds of thousands in the largest genomes.

Table 4.1 Genome size and coding content of different types oforganisms.

Species Domain Genome size(million bp)[a]

No of genes Coding (%)

Mycoplasma genitalium Bacteria 0.58 470 100Escherichia coli Bacteria 4.8 4 288 100Methanococcus jannaschii Archaea 1.7 1 738 100Saccharomyces cerevisiae Eukarya 12 6 144 70Caenorhabditis elegans Eukarya 100 18 266 25Arabidopsis thaliana Eukarya 100 25 498 31Homo sapiens Eukarya 3 400 32 000 28[b]

1.4[c]

Triticum aestivum Eukarya 17 000 60 000 Not determinedAmoeba dubia Eukarya 670 000 Not determined

a Million base pairs = number of nucleotides.b Total.c For proteins.

The very large genomes, e.g., those of wheat or amoebas, have not been sequenced.Therefore, their accurate sizes and gene contents are not known as yet but can beestimated from their physical properties. It is clear that genome sizes are correlatedwith neither the size nor the complexity of the different species. This seemingparadox is explained by the fact that the large eukaryotic genomes contain largeamounts of non-coding DNA. In humans, for instance, only about 1.5% of thegenomic DNA codes for protein products, and only about 28% of it is transcribedinto RNA. A large part of the remaining DNA is composed of highly repetitivesequences, which are often referred to as “junk-DNA.” However, the non-codingDNA is not all insignificant, because some of those sequences have importantfunctions as structural elements of the DNA or have contributed (or may contributein the future) to the evolution of the genome.Although the cellular genomes are very large, they function in very controlled

manner. Among all the multiple genes, and in the middle of the very large non-coding sequences, the functional genes are expressed in a highly coordinatedfashion: the amount, timing, and location of the expression of each gene areaccurately regulated. The gene regulation is mediated mostly by different proteins– but in many cases also by small, non-coding RNAs.Different proteins, RNAs, membranes, and small soluble molecules such as

sugars and salts fill up the cellular contents, up to a level of molecular crowding in


the interior space. Although the cellular contents are very complex, their centralfunctions are uniform between all different cells and between all species. Partic-ularly, the genetic code itself and its expression mechanism are the same, inprinciple, in all species (Fig. 4.5).

4.2.2.2 The Genetic Code and Its ExpressionThe genetic information is encoded in the nucleotide sequences in groups ofthree adjacent nucleotides, the codons, each corresponding to specific aminoacids (or a stop sign). Although the four nucleotides (A, G, C, and T in DNA;in RNA, T is replaced by U) can be organized into a total of 43 = 64 different tripletcombinations, only 20 different amino acids are utilized and coded for in thecurrent life forms – although some prokaryotes use 22 different amino acids.Thus, the coding system includes some redundancy: several codons code for thesame amino acid (Table 4.2). Each gene is composed of a set of triplet codons. Thecode of each gene (or the open reading frame, ORF) starts at a specific ATG tripletin the DNA and continues until it reaches one of the following triplets: TAG,TAA, or TGA, which do not code for any amino acid. These stop codons mark theend of the gene (Table 4.2). In eukaryotes the genes are often interrupted byintervening sequences (introns) that must be removed from the sequence duringits expression process.


Fig. 4.5 Flow chart of the expression of genetic information.


Table4.2

Thegene

ticcode

,com

posedof

triplets

ofthefour

nucleicacid

basesuracil(U

),cytosine

(C),ad

enine(A),

andgu

anine(G

),an

dtheirinform

ation(aminoacid

orstartor

stop

codo

n).

Firstbase

Cod

onSecond

base

UInform

ation

Cod

onSecond

base

CInform

ation

Cod

onSecond

base

AInform

ation

Cod

onSecond

base

GInform

ation

Thirdbase

U U U U

UUU

UUC

UUA

UUG

Phen

ylalan

ine

Phen

ylalan

ine

Leucine

Leucine

UCU

UCC

UCA

UCG

Serine

Serine

Serine

Serine

UAU

UAC

UAA

UAG

Tyrosine

Tyrosine

Stopcodo

nStopcodo

n

UGU

UGC

UGA

UGG

Cysteine

Cysteine

Stopcodo

nTryptop

han

U C A G

C C C C

CUU

CUC

CUA

CUG

Leucine

Leucine

Leucine

Leucine

CCU

CCC

CCA

CCG

Prolin

eProlin

eProlin

eProlin

e

CAU

CAC

CAA

CAG

Histidine

Histidine

Glutamine

Glutamine

CGU

CGC

CGA

CGG

Arginine

Arginine

Arginine

Arginine

U C A G

A A A A

AUU

AUC

AUA

AUG

Isoleu

cine

Isoleu

cine

Isoleu

cine

Methionine,

startcodo

n

ACU

ACC

ACA

ACG

Threon

ine

Threon

ine

Threon

ine

Threon

ine

AAU

AAC

AAA

AAG

Asparagine

Asparagine

Lysine

Lysine

AGU

AGC

AGA

AGG

Serine

Serine

Serine

Serine

U C A G

G G G G

GUU

GUC

GUA

GUG

Valine

Valine

Valine

Valine

GCU

GCC

GCA

GCG

Alanine

Alanine

Alanine

Alanine

GAU

GAC

GAA

GAG

Asparticacid

Asparticacid

Glutamic

acid

Glutamic

acid

GGU

GGC

GGA

GGG

Glycine

Glycine

Glycine

Glycine

U C A G

The genetic code is interpreted (or expressed) in a multi-step process (Fig. 4.5) thatconverts the sequence of the nucleotide triplets into a linear sequence of thecorresponding amino acids (Table 4.2). First, the sequence of the target gene iscopied (transcribed) into a messenger RNA (mRNA). The mRNA contains thesame sequence as the corresponding DNA, but in contrast to DNA, the RNApolymer is short-lived and is used only for short-term expression of the code.The mRNA associates with the two subunits of the ribosome, which then movesalong the mRNA and recognizes the triplet code, starting from the first AUG codonon the mRNA (corresponds to the ATG on the DNA). The nucleotide triplets arerecognized by the anticodon triplets of the aminoacylated transfer RNAs (tRNAs),which enter into the ribosome complex and bring in the specific amino acidscorresponding to each triplet codon. The peptide bonds between the adjacentamino acids are formed by the catalytic RNA component of the ribosome (riboso-mal RNA, rRNA). As these amino acids are brought into the reaction complex, theribosome joins them into a long chain or “translates” the nucleotide sequence intoan amino acid sequence (Fig. 4.5). The produced amino acid chain is initially calleda polypeptide, but after it folds into the accurate three-dimensional structure, itbecomes a functional protein.Thus, the components needed for the expression of the genetic code are the

mRNA, the tRNAs and the amino acids, and the ribosomes. The ribosome itself iscomposed of multiple proteins and RNAs (varying from 52 to 79 proteins and fromthree to four RNAs in different species). Each of the steps of the gene expression(transcription, tRNA amino acylation, and the translation itself) requires multipleaccessory proteins for correct function and regulation. This strong protein depend-ency of the whole gene expression process creates a dilemma similar to the one ofthe chicken and egg. Proteins are required for expression of the genetic code as wellas for the maintenance (or replication) of the code, and the code is needed for theexpression of the proteins. Thus, how could the genetic DNA first be generated andreplicated, and how was its expression machinery first established – how did thiscyclic process get started?It is assumed that the storage and expression of the genetic information were the

first hallmarks for life as we know it and that these were the key elements in themolecular evolution that led to the birth of the LUCA. They existed already at thetime of the LUCA, and they required functions such as genome replication,transcription and translation, and pathways for amino acid and nucleotide syn-thesis. These functions are so essential for present life that their origin is thecentral part of the question of the origin of life as a whole.

4.3Last Universal Common Ancestor (LUCA)

The features that occur in all life forms are essential to life. Therefore, they shouldhave been present already in the earliest established cellular life, i.e., in the LUCA.Such conserved features include


• the enclosure or containment in cell membranes,• the genetic code, and• the translation machinery for the expression of the code

(the ribosomes, tRNAs, and amino acids).

Some enzymes related to RNA and amino acid biosynthesis and degradation and toenergy production and use (cell metabolism) also are common to all cellular life. Afurther curious detail that is fully conserved in all cellular life is the symmetrybreaking, or homochirality, occurring in its central molecules: all the amino acidsused in the cellular proteins are of the same stereoisomer type, which is the left-handed (L)-configuration (see Chapter 2), and the deoxyribose and ribose sugarsused in all the nucleotides are of the right-handed (D)-configuration only, meaningthat the bond between the carbons in positions 4 and 5 points up, not down(Fig. 4.4).

4.3.1Containment in a Cell Membrane

As mentioned earlier, all life on Earth is cellular, which means that it is allcontained within, and separated from its environment by cell membranes. Thiscontainment is important for many reasons. Themolecules synthesized in the cellsdo not escape into the environment, and the concentrations of the intracellularmolecules are maintained at desired levels by regulating their synthesis anddegradation. Molecules from outside are transported in and out in a regulatedmanner, and the cellular molecules interact and function in amutually coordinatedway. Further, because the cell membrane physically connects the genomes withtheir respective gene products, the selection for beneficial products and functionsbecomes targeted to their corresponding coding sequences, i.e., the genes canevolve based on their products. The physical connection also allows the jointmaintenance of different segments of the genomes and allows their coevolutiontowards synergistic functions. All in all, the cell membrane allows all cellularcomponents to function and evolve as one coordinated entity and unit.The excellent utility of present-day membranes is related to their highly

sophisticated properties. Cell membranes are formed of amphiphilic (i.e., oneend is hydrophobic and the other end is hydrophilic) molecules called lipids,which aggregate in water and assemble into bilayers (see Chapter 3). These lipidbilayers are themselves impermeable to water, but they are spanned by severaldifferent proteins that serve as transport channels for water-soluble moleculesand as receptors for external signals and cues. The cells may also adjust theproperties of their membranes by changing their protein components or bychanging the saturation level of lipids according to temperature. Cells continu-ously produce new lipids for the growth of their membranes, and different lipidsare produced to construct membranes for different compartments. Thus, mem-branes in current cells are very dynamic and functional. However, the situationwas quite different at the time prior to the existence of the proteins needed for


lipid biosynthesis or for membrane transport channels. How could the cells becontained at this stage?It is possible that some type of membrane was formed in the early world by

spontaneous assembly of abiotically formed lipids. It has been shown that differentpolar hydrocarbon derivatives, containing 10 or more carbons in their hydrocarbonchain, are amphiphilic molecules that may assemble into bilayers, and these againmay spontaneously form vesicles in aqueous environments. Such aliphatic (or linear)and aromatic (or circular) hydrocarbons are present, for instance, in the carbonaceouschondrites (see Chapter 3). Hydrocarbon–lipid vesicles might have enclosed theearliest genomes and functioned as compartments for their replication. However,this scenario involves severe problems. Because the hydrophobic lipid membranesseparate the organism from the surroundings, they may prevent access to theirresources, such as useful molecules available in the surrounding. Further, becausethe organism is closed inside a “dead” membrane, it may not be able to expand ordivide or to allow its progeny to accumulate beyond its own original compartment.Several membrane chemists, e.g. the research groups of Deamer, Luisi, and

Szostak, have attempted to resolve the assembly and the functional parameters ofspontaneously assembled membrane vesicles. They have shown that the perme-ability of the bilayer membranes is related to the length of the aliphatic carbonchains: modified hydrocarbons of less than 14 carbons are permeable for smallionic molecules, such as amino acids and phosphates. Actually, lipid membranesformed of carbon chains of less than 10 carbons are too permeable to maintain anyion gradient. The membrane vesicles formed of longer fatty acids, such as oleicacid, are semipermeable: small molecules, such as nucleotides or amino acids, maydiffuse through them while large polymers may not. This property would allowspontaneous uptake of nucleotides into the vesicles and retention of the polymersinside them. This process would increase the osmotic potential inside of thevesicles and cause the growth of the membrane via incorporation of more fattyacids drawn from emptier vesicles or frommicelles. Thus, themere hydrophobicityof fatty acids or of other lipid molecules may have caused the prebiotic assemblyand function of primitive, cell-like structures. Indeed, assembly and growth, andeven division of such lipid vesicles, have been demonstrated in laboratory con-ditions. Likewise, nucleotide and amino acid polymerization inside the vesicle hasbeen induced, simulating the assembly of small, artificial cells.To have an adequate supply of the lipids (or of amphiphilic carbon chains) for

membrane assembly, the LUCA would have needed the pathways to synthesizecarbon chains containing at least 10 carbons. A significant dilemma related to theorigin of the lipid biosynthesis pathways is that in present life two completelydifferent types of lipids are used for cell membranes: the Archaea use isoprenoid-type carbon chains (polyunsaturated hydrocarbons with methyl side chains), andthe Bacteria and Eukarya use fatty acid–type (unbranched) carbon chains. Thesetypes of carbon chains are produced via completely different pathways, and thepathway utilized in Archaea does not even exist in Eukarya or in Bacteria. Thus, it isdifficult to deduce what kind of lipid biosynthesis might have been utilized in theLUCA and how this early membrane synthesis gave rise to two different mem-


brane compositions. It is possible either that several different lipid biosynthesispathways were established in the LUCA population, or that the cellular membranesynthesis pathways were established after the divergence of the three domains.However, this latter scenario would leave open the question of how, or in what, theLUCA was contained.It has been suggested by some geochemists that prebiotic reactions and early life

would have utilized some other types of compartments, formed of inorganic surfa-ces. W�chtersh�user (2003) has proposed that prebiotic chemistry might haveoccurred on surfaces of clays or minerals where the earliest cells might then haveassembled. These minerals would have catalyzed the reactions and stabilized theforming polymers (see Chapter 1). Martin and Russell (2002), Koonin and Martin(2005), and Brown propose that the porous, chimney-like structures of metal sulfide(mainly FeS) precipitates, formed at the hydrothermal vents at the bottom of theearly ocean, functioned as chemically rich, protective hatcheries that providedcontainment and suitable chemical conditions for the chemical evolution towardslife. The main attractions of these latter ideas are as follows.

• Firstly, those metal sulfide mounts were formed from amultitude of small, interconnected compartments, whichmight have served as containments for chemicals and ascatalytic surfaces for reactions.

• Secondly, the hydrothermal vents produced a continuousflow of warm geothermal fluid, full of several different re-duced chemicals, and it maintained a strong reduction gra-dient between the H+-rich geothermal fluid and (supposedly)alkaline seawater, driving the reduction chemistry of themolecules.

• Thirdly, the hydrothermal vents produced a temperaturegradient, providing convection flows to cycle the macromo-lecules between double-stranded and single stages (discussedin Section 4.6).

The combination of all these factors might have allowed the evolution of complexmolecular communities in the cell-like inorganic compartments, until they wereadequately competent to produce lipids and proteins for cellular membranes andstructures and might escape from the hatchery to self-sustained life in the outsideworld.

4.3.2Genes and Their Expression

One experimental way to study what properties and functions were present in theLUCA is to look at which genes or sequences are still common to all the organismswhose sequences are known today (assumably derived from the common origin).Lazcano and coworkers compared a set of fully sequenced genomes and found 283genes that are highly conserved in all Eukarya genomes, 24 that are highly


conserved in Bacteria, and 145 that are conserved in Archaea. In all domains thesegenes include putative ATPases (for conversion of proton gradients into adenosinetriphosphate [ATP] synthesis and for utilizing the energy of ATP), genes involvedin transcription and translation, as well as RNA helicase and enolase, phosphor-ibosyl pyrophosphate synthase, and thioredoxin genes, which are involved innucleotide biosynthesis and RNA degradation. Such genes, if they were presentin the LUCA, indicate that the organism possessed means for maintaining itsgenetic information (at least in RNA form) and a translation system. Because theATPases locate in the membranes and produce ATP (as energy compound) byutilizing proton gradients formed across the membranes, this indicates that LUCAhad a cell membrane and produced and used energy in the form of ATPmolecules.Another approach to model primitive life is to analyze what would be the

minimal set of genes required by the simplest cells today. Several groups ofbioinformatists have worked on such questions. Gill and coworkers have searchedthe genomes of the smallest existing cells (bacterial and archaeal species, whichlive as endoparasites inside their host cells) for the set of genes that seemmandatory for them all. The living environments of these species are chemicallyvery rich, and the cells may obtain a large part of all their required biochemicalprecursors from their hosts. Therefore, they have lost the corresponding genesfrom their own genomes and have evolved, by reduction, towards ultimately smallgenomes. Comparison of the genomes of such species revealed that they have 206genes in common. All species have additional genes that allow them to survive intheir specific environment (host), but these 206 genes seem to comprise theobligatory set of genetic information required in all these species. Thus, it canbe reasoned that a comparable set of genes is essential for any cellular life, evenwhen living in the most protected and nutrient-rich conditions. Thus, if the LUCAwas a well-established cellular species, sustained in its own (probably chemicallyrich, easy, and protected) environment, it probably had to possess at least thisnumber of gene different functions.As the early organisms evolved to more complex, the initial sequences were

converted via mutation and recombination to code for new functions. The genomesgrew larger by duplicating, recombining, and modifying what they already had:new genes were often produced from previously existing ones, by recombining andmodifying functional protein domains (3-dimensional structures). Recent proteinstructure analysis by Doolittle and coworkers has identified a set of 49 protein-folding domains (or folding super-families) that are present in all analyzed ge-nomes of the three domains of life, suggesting that these protein-folding structureswere already present in the LUCA. Again, these protein structures occur in theproteins related to translation and to metabolic and glycolytic enzymes.So far, it has been reasoned that LUCA was a fairly complex organism. But how

did it diversify into the three domains of life that we know today? The threedomains differ from each other in such ways that their direct descent from oneanother, in a fixed order, is difficult. Each pair of domains shares some featuresthat are lacking from the third domain (Fig. 4.6), so it seems that none of them isdirectly derived from the others.


Because the deviation of the three domains from the LUCA is difficult to traceback, the question of the order of the establishment of the three domains remainsopen, i.e.:

• whether the prokaryotes differentiated as two branches fromthe LUCA and then formed the eukaryotes later by mutualfusion;

• whether the eukaryotes were derived directly from the LUCAand later gave rise to the prokaryotes (e.g., by plasmid escapeand reduction processes); or

• whether the three domains diverged separately from a mixedLUCA population.

When this question has been addressed by phylogenetic studies, different resultshave been obtained from different genes. For instance, the classical phylogenetictree based on 16S-rRNA sequences, first produced by Woese and coworkers in1990, shows the early deviation of the Bacteria and Archaea domains, with thethermophilic Bacteria and Archaea at the base of the different branches, and thelater deviation of the Eukarya domain from the Archaea (Fig. 4.7A). However, someauthors, e.g., Poole and Forterre, suggest that the phylogenetic analysis may notaccurately resolve the most ancient sequences: after very long (or very fast)evolution, sequences may become so saturated with mutations that they appearas more conserved in the phylogenetic analysis.When different protein gene sequences are analyzed, diverse phylogenetic trees

are produced for the different sequences. This may indicate that the domains havenot evolved as separate lines but rather that the genes have been mixed by stronglateral gene transfer after the separation of the domains.It is now widely discussed (see reviews by Pennisi and Doolittle) that the

intensive lateral gene transfer between species, and even between domains, mayhave mixed the initial lineages so effectively that it may be difficult to trace back anyoriginal sets of genes associated with the early phylogenetic lines. Such lateral genetransfer would have been possible because the newly separated lineages were stillvery simple, similar, flexible (nonspecific), and rudimentary in their functions.Therefore, they might utilize the same novel functions and structures, even if those


Fig. 4.6 Distribution of some key conservedfeatures among the three domains of life: eachof them is shared by two domains only.

were transferred across the domain borders. The DNA exchange could have beenmediated via cell fusions or via direct DNA uptake (gene transfer or cellularconjugation) – or via third parties, such as viruses or plasmids (gene transductionor transformation).Particularly in eukaryotes, the uptake of foreign (prokaryotic) DNA may happen

via eating up (endocytosis) of foreign cells. This process is still a distinct function of


Fig. 4.7 Phylogenetic lineage of the three domains of lifedetermined by different genetic sequences. (A) 16S ribosomalRNA sequence (adapted from Woese et al. 1990); (B) severaldifferent sequences (adapted from Doolittle 1999).

some eukaryotic cells. Mitochondria and chloroplasts are well-known examples,indicating that endocytosis of other species has occurred in the history of differenteukaryotes. In these instances the engulfed prokaryotes were maintained intact inthe cytoplasm and established as beneficial endosymbionts, or organelles, of thecells. Considering the strong lateral gene transfer, the tree of life at its earlier stageslooks rather like a bush (Fig. 4.7B).

4.3.3Hypothetical Structure of the LUCA Genome

The dilemma of the differentiation of the three domains relates to the question of thetype and structure of the LUCA genome. It is commonly thought that LUCA shouldhave been similar to the simplest life forms existing today, the prokaryotes. Accord-ingly, it should have been driven by a small, circular DNA genome. However, Pooleand Forterre and their coworkers argue that the circular, supercoiled prokaryoticgenomes with a single origin of replicationmight represent a later adaptation to veryfast and efficient replication strategies.The most primitive DNA genomes may havebeen linear, like the RNA genomes (see Section 4.4), which are thought to havepreceded the DNA genomes. One argument supporting the idea that the eukaryote-like linear genome structure is themost original one is that specific catalytic RNAs –apparent relicts of the earlier RNA genomes – are still used to process different RNAproducts in the eukaryotes (Table 4.3), while many of them have been replaced bymore efficient (and advanced) protein catalysts in the prokaryotes. Likewise, tRNA-like components are still utilized in the enzymes (telomerases) that maintain thetermini (telomeres) of the linear eukaryote chromosomes, suggesting that theseterminal structures are derived from the genomes of RNA-based life.The primitive RNA genomes may have influenced the ploidy level (the copy

number) and the fragmentation (chromosome number) of the later-arriving DNAgenomes. The early RNA genomes were very fragile and prone to degradation, andthe inaccurate replication processes accumulated multiple mistakes in their se-quences. For these reasons, the genomic components did not grow very large. Inorder to accumulate more coding capacity, the genomes should have been com-posed of multiple short components. To avoid the loss of genetic information dueto high mutation rates, the cells should have maintained more than one copy ofeach genomic component, and thus diploid (or maybe multiploid) rather thanhaploid (prokaryote-like) genomes should have been used (although one has tobear in mind that prokaryotes also normally maintain several copies of theirgenome in each cell). The earlier RNA-genome strategy may have been maintainedafter conversion to the DNA form, suggesting that the earliest cellular genomesshould have been composed of multiple, short, linear components, each presentedin more than a single copy.It is not clear whether the LUCA had evolved, as yet, to the DNA stage, or

whether the transition from RNA to DNA genomes occurred separately in the threedifferent lineages after their separation from the LUCA. Later conversion fromRNA to DNA genomes may be supported by the fact that different types of DNA



Table4.3

Exam

ples

ofpresen

t-da

yRNAcatalystsan

dotherfunction

alRNAs.

RNA

Function

Distribution

Putative

occurren

cein

theRNA

orRNPworld

Ribosom

alRNAs

Translation:structuralan

dcatalytic

Ubiqu

itou

sYes

mRNAs

Carriersof

thegenetic

code

Ubiqu

itou

sYes

tRNAs

Translation:A

minoacid

tran

sport

Ubiqu

itou

sYes

tRNA

Aminoacid

metabolism

Ubiqu

itou

sYes

tRNA

Replicationprim

erRetrotran

sposon

s,retroviruses,

pararetroviruses

Possibly

Telom

eraseRNA

tRNA-like

prim

erforchromosom

een

dsynthesis

Eukaryotes

Yes

RNaseP

tRNAmaturation

Ubiqu

itou

sYes

snoR

NAs

rRNAprocessing

Eukaryotes,som

eArchaea

Yes

RNaseM

RP

rRNAprocessing

Eukaryotes

Related

toRnaseP

GroupIself-splicingintron

smRNAsplicing

Eukaryotes,som

eProkaryotes

Possibly

GroupII

self-splicingintron

smRNAsplicing

Eukaryotes,som

eProkaryotes

Possibly

srpR

NA

Protein

tran

slocation

Eukaryotes,som

eArchaea

Yes

vaultRNA

Not

know

n–Protein

tran

slocation?

Eukaryotes

Possibly

G8RNA

Maintenan

ceof

ribo

somal

apparatus

atelevated

temperatures

Eukaryotes

Probably

Ham

merheadan

dhairpin

ribo

-zymes

Self-cleavage

andlig

ation

Viroids

andsatRNAs

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polymerases are utilized by Bacteria and by Archaea and Eukarya. Also, if the RNAgenomes were stabilized via methylation of the 2’ hydroxyl groups of the ribosemolecules, as suggested by Poole, it is conceivable that the RNA genomes mighthave developed to be fairly large, gaining significant coding capacity. Such RNAgenomes may have been adequate to support self-sustained cellular life and toproduce codes for the ribonucleotide reductases, thymidylate synthases, and re-verse transcription enzymes eventually needed to convert the ribonucleotides intodeoxyribonucleotides and RNA sequences into DNA. Forterre suggests that thoseDNA-producing enzymes and, consequently, DNA genomes were invented severaltimes to establish DNA-based viral genomes colonizing the RNA cells and that theywere transferred from those to the RNA-based host cells, in three separate transferevents, to establish the three DNA-based domains of life.Woese has suggested that at the earliest stage of evolution, when the genomes

were still very small and unstable, the fully functional genetic information couldnot exist in individual discrete organisms or genomes. He suggests that these earlygenomes instead formed a diverse community of organisms that dynamicallyinteracted with each other, exchanging, testing, storing, and evolving alternativegenomic sequences. Woese calls these early life forms “progenotes,” which de-scribes the evolutionary stage preceding the fixed genomic life forms, or the“genotes.” Again, it is not clear whether such progenotes would have had a DNAor an RNA genome; maybe they could have been characteristic both before andafter the transition from RNA to DNA genomes.

4.4“Life” in the RNA–Protein World: Issues and Possible Solutions

LUCA appears to have been a fairly complex and well-established organism – butfrom where did this complexity arise? Information flow from DNA into mRNA andthen into proteins (Fig. 4.5) demands multiple functions in between; therefore, it iscommonly thought that the whole genetic machinery had to evolve from a simplersystem. It is supposed that the genetic system preceding the DNA genomes wereRNA genomes, which could have functioned as information storage media and astemplates for translation. It is thought that the protein synthesis became estab-lished at the time of the RNA genomes and that the appearance of the proteincatalysts then allowed the “invention” and establishment of the DNA genomes.Thus, present-day DNA–RNA–protein life would have been preceded by lifecomposed of RNAs and their encoded protein products – or by RNA–protein(RNP) life.At the earliest stages, when the genetic code was translated into protein products,

or the genetically encoded proteins were “invented,” both the codes and theirexpression system were certainly very primitive. The codes had not yet evolved tocode for specific functions, and also the translation system was very inaccurate.Maybe only a few of the currently known amino acids were used. The system wasable to produce only a few short, nearly random polypeptides. The polypeptides had


not been adapted to specific functions, but maybe some of them could bind to RNAand function as scaffolding or structural proteins, similar to present-day chaper-ones. Such structural proteins may still have been quite useful in stabilizing theRNA genomes and in holding them in suitable three-dimensional structures toenhance their catalytic properties. Such structural proteins probably assisted in themost essential functions of the RNP world, i.e., in the replication of the RNAs. Thehigh mutation rate produced more functional gene products, and in due coursesome proteins appeared that actually catalyzed the replication of RNA genomes.

4.4.1Evolutionary Solutions

The early enzymes were still very inefficient and prone to errors. Therefore, eachtime the genomes were replicated, considerable portions of the nucleotides werecopied wrong and the genetic information was altered. If the sequences mutatedtoo much, it was changed into a non-functional form, the gene was no longermaintained, and the information was totally lost. This critical level of accumulationof errors has been defined by Manfred Eigen as the “error threshold” and is nowknown as the “Eigen limit.” The number of incorrectly copied nucleotides in-creased with the genome length; the longer the genomes, the easier they accumu-lated fatal levels of mistakes. Thus, only fairly short genomes (or genomic compo-nents) could be maintained by this very error-prone replication.Eigen has demonstrated how the evolution of small genomes (e.g., viral ge-

nomes) functions in a cyclic fashion, where repeated improvements of differentsynergistic functions lead to very efficient improvement of fitness and adaptationto new conditions. As described by Poole, this cyclic adaptation and genome-building model seems applicable for the gradual improvement of the RNP organ-isms: the new sequence variants encoded for improved replicase proteins or newcomponents for the translation machinery. These produced better replicase mol-ecules and thereby improved the accuracy of the replication. This again allowed themaintenance of longer genomes – and the increasing coding capacity allowed forthe production of new components for the replication and translation machineries.


Fig. 4.8 Darwin–Eigen cycle demonstratingthat Darwinian selection for improved repli-cation and translation allowed maintenanceof larger genomes, and these again allowedfor improved replication and gene expression.Thus, the increasing genome size, new genefunctions, and improving replication andtranslation fidelity have mutually enhancingeffects on the evolution of complexity (adaptedfrom Poole et al. 1999).

Thus, Darwinian selection for more accurate replication and the correspondingincrease of the genome size (determined by the Eigen limit) together enhanced theevolution towards more complex genomes (Fig. 4.8).

4.4.2Solutions Found in the Viral World

It is of interest that present-day single-stranded (ss) RNA viruses possess multiplefeatures that seem similar to the properties of a hypothetical early RNP organisms.As in the RNP organisms, the viral genomes are composed of short linear RNAsthat code only for a few necessary gene products. The total length of RNA virusgenomes seems to be limited by both the fragility of the RNAs and the Eigen limit(the avoidance of accumulating too many errors by inaccurate replication); thus, atthe present time the longest ss RNA virus genomes – those of the coronaviruses –contain about 30 000 nucleotides. The smallest viral genomes, – those of theleviviruses – are only about 3 500 nucleotides long and code only for three proteins,namely, the replicase protein, the coat protein, and a maturase protein to interactwith the host. These seem to make the minimal protein set required for sustainableviral genomes. In many viruses the replicase proteins are divided in two separatecomponents, the helicase and the replicase, apparently because those proteins needto be produced in very different amounts.The coat protein is required to enclose the RNA and to protect it from degrada-

tion. All viruses encode one or more of other gene products to interact with theirhost cells – mainly in order to suppress the host defense functions – but it appearsthat in principle the replication and the protective functions are the most importantrequirements for viral survival. This may also indicate how important theseproteins may have been to the early RNA replicators.Viruses maximize the use of their limited genomic sequences – they use them in

the most efficient way. They contain a minimal amount of non-coding sequences,and they do not “invest” any coding capacity for producing regulatory proteins,which are so essential for cellular life. Many viruses regulate their essentialfunctions – initiation of replication and translation – by short and simple sequen-ces at the termini of the RNA genomes and by interactions between RNA loops andsequences. With such RNA interactions, some viruses are capable of dedicatingtheir genomic RNAs to function in either the replication or the translation mode,which avoids collision of the two opposite processes.Being parasites of the cellular world, RNA viruses make their living in a chemi-

cally rich environment: the host cells provide all the building blocks of the macro-molecules (the nucleotides and the amino acids) and the translation machinery foruse by the viruses. Likewise, the early RNP organisms had to live in a similarenvironment, because they had no means for synthesizing their own buildingblocks. Through their evolutionary history, the RNA viruses have become veryefficient in their replication and in their adaptation to their own specific hostorganisms. Indeed, in spite of their ultimately minimal size, the RNA viruses arevery successful. There are many more species of viruses than there are cellular


species, and each cellular species may be infected by several different viral species.It is possible that the (fully evolved) RNP-based life forms were efficient andsuccessful replicators. Apparently they had to be quite advanced in order toproduce adequately large genomic pools to give rise to DNA-based life and cellularorganisms. Some of the early RNP-based replicators may have survived to form thebase for the massive variation of present-day viruses.

4.5“Life” Before the Appearance of the Progenote

4.5.1The Breakthrough Organism and the RNA–Protein World

The first protein-mediated functions initiated evolution towards more and morecomplex biochemistry. Therefore, the initiation of genetically encoded proteinsynthesis has been the key step in the development of any more-advanced life.This event has been considered so essential that Poole and coworkers have namedthe first creature that produced proteins the “breakthrough organism.” But howcould this hypothetical breakthrough organism break through – or, how might ithave come into existence in the first place?Clearly, it had to evolve from simpler systems through a cascade of improving

stages. It was required that it be able to synthesize mRNA-like translatablesequences and to run a primitive translation machinery consisting of ribosomes,tRNAs, and amino acids. Because protein synthesis did not exist prior to this time,the assembly or function of this primitive translation machinery could not havedepended on any specific proteins. Thus, the early translation reactions had to becatalyzed by the existing RNAs alone. This is theoretically feasible because in all thepresent-day life forms, the formation of the peptide bonds between amino acids isspecifically mediated by one RNA component of the ribosomes. Different naturalor in vitro–selected RNA molecules may catalyze many other reactions (for thenatural ribozymes, see Table 4.3). For instance, ribozymes have been found thatcan mediate the amino acylation of tRNAs. Thus, according to experimental data, itmay be postulated that mere RNA components were able to mediate the earliesttranslation process.

4.5.2Primitive Translation Machinery

A logical requirement for the existence of RNA-based translation machinery is thatthis machinery itself was initially generated and maintained in a protein-independ-ent manner. Present-day ribosomes are massive complexes, containing either three(in prokaryotes) or four (in eukaryotes) RNAs that vary in size from 120 to 2 904nucleotides. The genes coding for these RNAs take, together with their interveningsequences, more than 7 500 nucleotides of genomic sequences. It is clear that the


earliest RNA components were not as long as they are today. As mentioned inSection 4.4.1, the error-prone replication systems produced only fairly short RNAstrands that are estimated not to have exceeded a few hundred nucleotides in length.Thus, it is likely that the proto-ribosome had to be composed of short fragments ofRNA that jointly formed one functional complex. This may still be evident inpresent-day ribosomes, because their interaction with tRNAs may be mimicked bya separate small RNA analogue of the ribosomal RNA sequence and because peptidebond formation is catalyzed by a specific adenine in the core of the ribosomal RNA.Thus, it seems likely that the present-day ribosomal RNAs (rRNAs) developed via acombination of previously existing, small functional subunits.

4.5.3Origin of Ribosomes

Even if the early ribosomes were formed of small separate RNAs, their mainte-nance required that they be reproduced fairly accurately. The mere existence ofsuch a functional complex required that it had evolved gradually from somesimpler structures – which again had been maintained and selected for their

4.5 “Life” Before the Appearance of the Progenote 109

Fig. 4.9 Model of the early function of the proto-translationmachinery as RNA replication complex (from Poole et al. 1998,with permission from the publisher).

preexisting function(s). The most important function at this stage would have beenthe maintenance of the existing sequences, namely, the replication of RNAs. Pooleand coworkers have proposed that the original function of the proto-ribosomalcomplex was the replication of RNAs. According to their model, the early proto-ribosomes extended the complementary RNA strand on the RNA template byligating nucleotide triplets (corresponding to present-day anticodon loops) broughtinto the reaction by tRNAmolecules or their primitive precursors. This means thatearly replication was mediated by ligation rather than by polymerization. Incorpo-ration of nucleotide triplets rather than single nucleotides had the advantage ofallowing higher affinity and longer-lasting annealing of the incoming nucleotidesto the template. This allowed more time for the very slow RNA catalyst to performthe ligation (Fig. 4.9).According to this model, it is conceivable that amino acid acylation of the incom-

ing tRNAs was a significant step in the early replication process. The covalentbinding of the amino acids to the -CCA terminus of the tRNAs might have chargedthese molecules with energy, which might have been released by the detachment ofthe amino acid during the polymerization. This process might have been used todrive the polymerization. On the other hand, it is conceivable that the positivelycharged amino acids allowed the proper confirmation (tight folding) of the primitive(negatively charged) tRNAs and/or allowed their binding to the replicase complex.Release of the amino acids from the tRNAs might then have caused a conforma-tional change allowing for the release of the used tRNA from the complex.In any of these scenarios, the interaction between template RNA, ribosome, the

“triplet-reading” anticodons of the tRNAs, and the amino acids would have alreadybeen established at the early RNA replication function, prior to the invention ofprotein synthesis. Peptide bond formation might have been initiated as a sponta-neous reaction between the amino acids brought to close proximity by the incom-ing tRNAs. However, later conversion of the whole replication machinery into atranslation function is difficult to conceive – many things would be have beenrequired to change. For example, the hypothetic cleavage and ligation of thenucleotide triplets from the tRNAs and into the growing chain of RNA neededto be stopped and replaced by peptide bond formation. However, it is conceivablethat the introduction of protein synthesis made these changes possible, as itprovided protein catalysts for replication and a strong selection for the use ofribosomes for translation. Both processes, translation and replication, had to bemade to function on the same template in opposite directions. The function of thesame template in both replication and translation seems not to be a major obstacle,as it occurs in all present-day viruses in a coordinated and regulated fashion.Another model for the early role of tRNAs proposed byWeiner andMaizels is the

terminal taging of the replicating RNAs. These terminal tags would have func-tioned as the selective binding and initiation site of the replicase and thereby wouldhave helped to replicate the genomic ends correctly. This hypothesis is supportedby the fact that many present-day viruses have tRNA-like 3’ termini and thetelomerase enzyme that synthesizes the ends of the eukaryotic chromosomesfunctions on a tRNA-like template.


4.6The RNA World

Logically, it is necessary to assume that prior to the invention of protein synthesis,all reactions required for maintenance of macromolecules – and for their evolutiontowards life – had to be mediated by molecules other than proteins. Present-dayRNA chemistry has demonstrated that different RNA molecules (either naturalones or selected in vitro) may mediate several different catalytic activities, althoughthe RNA catalysts typically function less efficiently than protein enzymes, i.e., at amuch slower rate (Fig. 4.2). Such molecules are called RNA enzymes or ribozymes.Most of the naturally occurring ribozymes mediate cleavage and ligation reactionsof their target RNAs (Table 4.3). The smallest ribozymes contain about 50 nucleo-tides and occur in the RNAs of viroids and viral satellite RNAs, while complexribozymes capable of many different catalytic functions can be artificially producedby in vitro selection.It must be emphasized that the functionality of the RNA catalysts is based on the

sequence information. The information does not code for any protein products, butit dictates the folding of the RNA into secondary structures that can recognize theirsubstrates and cause the desired reactions. Figure 4.10 shows the three-dimen-sional folding structure, the so-called hammerhead structure, of the smallestnatural ribozymes, which are composed of about 50 nucleotides.Figure 4.11 gives an example of the evolution of an RNA polymerase ribozyme,

as mediated by in vitro selection steps. The class I ligase ribozyme catalyzes thejoining of the 3’ end of an RNA strand to the 5’ end of the ribozyme (Fig. 4.11 a);the class II ligase ribozyme catalyzes the addition of three nucleotide 5’ triphos-phates (NTPs) to the 3’ end of the primer, directed by an internal template


Fig. 4.10 Three-dimensional folding structure(so-called hammerhead structure) of the small-est natural ribozymes. These self-cleaving and-ligating structures occur in several viroid andviral satellite RNAs and are composed of about50 nucleotides.